LiverNet: efficient and robust deep learning model for automatic diagnosis of sub-types of liver hepatocellular carcinoma cancer from H&E stained liver histopathology images

  • Aatresh, A. A.
  • Alabhya, K.
  • Lal, S.
  • Kini, J.
  • Saxena, P. U. P.
Int J Comput Assist Radiol Surg 2021 Journal Article, cited 0 times
Website
PURPOSE: Liver cancer is one of the most common types of cancers in Asia with a high mortality rate. A common method for liver cancer diagnosis is the manual examination of histopathology images. Due to its laborious nature, we focus on alternate deep learning methods for automatic diagnosis, providing significant advantages over manual methods. In this paper, we propose a novel deep learning framework to perform multi-class cancer classification of liver hepatocellular carcinoma (HCC) tumor histopathology images which shows improvements in inference speed and classification quality over other competitive methods. METHOD: The BreastNet architecture proposed by Togacar et al. shows great promise in using convolutional block attention modules (CBAM) for effective cancer classification in H&E stained breast histopathology images. As part of our experiments with this framework, we have studied the addition of atrous spatial pyramid pooling (ASPP) blocks to effectively capture multi-scale features in H&E stained liver histopathology data. We classify liver histopathology data into four classes, namely the non-cancerous class, low sub-type liver HCC tumor, medium sub-type liver HCC tumor, and high sub-type liver HCC tumor. To prove the robustness and efficacy of our models, we have shown results for two liver histopathology datasets-a novel KMC dataset and the TCGA dataset. RESULTS: Our proposed architecture outperforms state-of-the-art architectures for multi-class cancer classification of HCC histopathology images, not just in terms of quality of classification, but also in computational efficiency on the novel proposed KMC liver data and the publicly available TCGA-LIHC dataset. We have considered precision, recall, F1-score, intersection over union (IoU), accuracy, number of parameters, and FLOPs as metrics for comparison. The results of our meticulous experiments have shown improved classification performance along with added efficiency. LiverNet has been observed to outperform all other frameworks in all metrics under comparison with an approximate improvement of [Formula: see text] in accuracy and F1-score on the KMC and TCGA-LIHC datasets. CONCLUSION: To the best of our knowledge, our work is among the first to provide concrete proof and demonstrate results for a successful deep learning architecture to handle multi-class HCC histopathology image classification among various sub-types of liver HCC tumor. Our method shows a high accuracy of [Formula: see text] on the proposed KMC liver dataset requiring only 0.5739 million parameters and 1.1934 million floating point operations per second.

Two-phase multi-model automatic brain tumour diagnosis system from magnetic resonance images using convolutional neural networks

  • Abd-Ellah, Mahmoud Khaled
  • Awad, Ali Ismail
  • Khalaf, Ashraf AM
  • Hamed, Hesham FA
EURASIP Journal on Image and Video Processing 2018 Journal Article, cited 0 times
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Three-dimensional visualization of brain tumor progression based accurate segmentation via comparative holographic projection

  • Abdelazeem, R. M.
  • Youssef, D.
  • El-Azab, J.
  • Hassab-Elnaby, S.
  • Agour, M.
PLoS One 2020 Journal Article, cited 0 times
Website
We propose a new optical method based on comparative holographic projection for visual comparison between two abnormal follow-up magnetic resonance (MR) exams of glioblastoma patients to effectively visualize and assess tumor progression. First, the brain tissue and tumor areas are segmented from the MR exams using the fast marching method (FMM). The FMM approach is implemented on a computed pixel weight matrix based on an automated selection of a set of initialized target points. Thereafter, the associated phase holograms are calculated for the segmented structures based on an adaptive iterative Fourier transform algorithm (AIFTA). Within this approach, a spatial multiplexing is applied to reduce the speckle noise. Furthermore, hologram modulation is performed to represent two different reconstruction schemes. In both schemes, all calculated holograms are superimposed into a single two-dimensional (2D) hologram which is then displayed on a reflective phase-only spatial light modulator (SLM) for optical reconstruction. The optical reconstruction of the first scheme displays a 3D map of the tumor allowing to visualize the volume of the tumor after treatment and at the progression. Whereas, the second scheme displays the follow-up exams in a side-by-side mode highlighting tumor areas, so the assessment of each case can be fast achieved. The proposed system can be used as a valuable tool for interpretation and assessment of the tumor progression with respect to the treatment method providing an improvement in diagnosis and treatment planning.

Robust Computer-Aided Detection of Pulmonary Nodules from Chest Computed Tomography

  • Abduh, Zaid
  • Wahed, Manal Abdel
  • Kadah, Yasser M
2016 Journal Article, cited 5 times
Website
Detection of pulmonary nodules in chest computed tomography scans play an important role in the early diagnosis of lung cancer. A simple yet effective computer-aided detection system is developed to distinguish pulmonary nodules in chest CT scans. The proposed system includes feature extraction, normalization, selection and classification steps. One hundred forty-nine gray level statistical features are extracted from selected regions of interest. A min-max normalization method is used followed by sequential forward feature selection technique with logistic regression model used as criterion function that selected an optimal set of five features for classification. The classification step was done using nearest neighbor and support vector machine (SVM) classifiers with separate training and testing sets. Several measures to evaluate the system performance were used including the area under ROC curve (AUC), sensitivity, specificity, precision, accuracy, F1 score and Cohen-k factor. Excellent performance with high sensitivity and specificity is reported using data from two reference datasets as compared to previous work.

A generalized framework for medical image classification and recognition

  • Abedini, M
  • Codella, NCF
  • Connell, JH
  • Garnavi, R
  • Merler, M
  • Pankanti, S
  • Smith, JR
  • Syeda-Mahmood, T
IBM Journal of Research and DevelopmentIbm J Res Dev 2015 Journal Article, cited 19 times
Website
In this work, we study the performance of a two-stage ensemble visual machine learning framework for classification of medical images. In the first stage, models are built for subsets of features and data, and in the second stage, models are combined. We demonstrate the performance of this framework in four contexts: 1) The public ImageCLEF (Cross Language Evaluation Forum) 2013 medical modality recognition benchmark, 2) echocardiography view and mode recognition, 3) dermatology disease recognition across two datasets, and 4) a broad medical image dataset, merged from multiple data sources into a collection of 158 categories covering both general and specific medical concepts-including modalities, body regions, views, and disease states. In the first context, the presented system achieves state-of-art performance of 82.2% multiclass accuracy. In the second context, the system attains 90.48% multiclass accuracy. In the third, state-of-art performance of 90% specificity and 90% sensitivity is obtained on a small standardized dataset of 200 images using a leave-one-out strategy. For a larger dataset of 2,761 images, 95% specificity and 98% sensitivity is obtained on a 20% held-out test set. Finally, in the fourth context, the system achieves sensitivity and specificity of 94.7% and 98.4%, respectively, demonstrating the ability to generalize over domains.

Computer-aided diagnosis of clinically significant prostate cancer from MRI images using sparse autoencoder and random forest classifier

  • Abraham, Bejoy
  • Nair, Madhu S
Biocybernetics and Biomedical Engineering 2018 Journal Article, cited 0 times
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Computer-aided classification of prostate cancer grade groups from MRI images using texture features and stacked sparse autoencoder

  • Abraham, Bejoy
  • Nair, Madhu S
Computerized Medical Imaging and Graphics 2018 Journal Article, cited 1 times
Website

Automated grading of prostate cancer using convolutional neural network and ordinal class classifier

  • Abraham, Bejoy
  • Nair, Madhu S.
Informatics in Medicine Unlocked 2019 Journal Article, cited 0 times
Website
Prostate Cancer (PCa) is one of the most prominent cancer among men. Early diagnosis and treatment planning are significant in reducing the mortality rate due to PCa. Accurate prediction of grade is required to ensure prompt treatment for cancer. Grading of prostate cancer can be considered as an ordinal class classification problem. This paper presents a novel method for the grading of prostate cancer from multiparametric magnetic resonance images using VGG-16 Convolutional Neural Network and Ordinal Class Classifier with J48 as the base classifier. Multiparametric magnetic resonance images of the PROSTATEx-2 2017 grand challenge dataset are employed for this work. The method achieved a moderate quadratic weighted kappa score of 0.4727 in the grading of PCa into 5 grade groups, which is higher than state-of-the-art methods. The method also achieved a positive predictive value of 0.9079 in predicting clinically significant prostate cancer.

A novel CAD system to automatically detect cancerous lung nodules using wavelet transform and SVM

  • Abu Baker, Ayman A.
  • Ghadi, Yazeed
International Journal of Electrical and Computer Engineering (IJECE) 2020 Journal Article, cited 0 times
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A novel cancerous nodules detection algorithm for computed tomography images (CT - images ) is presented in this paper. CT -images are large size images with high resolution. In some cases, number of cancerous lung nodule lesions may missed by the radiologist due to fatigue. A CAD system that is proposed in this paper can help the radiologist in detecting cancerous nodules in CT -images. The proposed algorithm is divided to four stages. In the first stage, an enhancement algorithm is implement to highlight the suspicious regions. Then in the second stage, the region of interest will be detected. The adaptive SVM and wavelet transform techniques are used to reduce the detected false positive regions. This algorithm is evaluated using 60 cases (normal and cancerous cases), and it shows a high sensitivity in detecting the cancerous lung nodules with TP ration 94.5% and with FP ratio 7 cluster/image.

Repeatability of Automated Image Segmentation with BraTumIA in Patients with Recurrent Glioblastoma

  • Abu Khalaf, N.
  • Desjardins, A.
  • Vredenburgh, J. J.
  • Barboriak, D. P.
AJNR Am J Neuroradiol 2021 Journal Article, cited 0 times
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BACKGROUND AND PURPOSE: Despite high interest in machine-learning algorithms for automated segmentation of MRIs of patients with brain tumors, there are few reports on the variability of segmentation results. The purpose of this study was to obtain benchmark measures of repeatability for a widely accessible software program, BraTumIA (Versions 1.2 and 2.0), which uses a machine-learning algorithm to segment tumor features on contrast-enhanced brain MR imaging. MATERIALS AND METHODS: Automatic segmentation of enhancing tumor, tumor edema, nonenhancing tumor, and necrosis was performed on repeat MR imaging scans obtained approximately 2 days apart in 20 patients with recurrent glioblastoma. Measures of repeatability and spatial overlap, including repeatability and Dice coefficients, are reported. RESULTS: Larger volumes of enhancing tumor were obtained on later compared with earlier scans (mean, 26.3 versus 24.2 mL for BraTumIA 1.2; P < .05; and 24.9 versus 22.9 mL for BraTumIA 2.0, P < .01). In terms of percentage change, repeatability coefficients ranged from 31% to 46% for enhancing tumor and edema components and from 87% to 116% for nonenhancing tumor and necrosis. Dice coefficients were highest (>0.7) for enhancing tumor and edema components, intermediate for necrosis, and lowest for nonenhancing tumor and did not differ between software versions. Enhancing tumor and tumor edema were smaller, and necrotic tumor larger using BraTumIA 2.0 rather than 1.2. CONCLUSIONS: Repeatability and overlap metrics varied by segmentation type, with better performance for segmentations of enhancing tumor and tumor edema compared with other components. Incomplete washout of gadolinium contrast agents could account for increasing enhancing tumor volumes on later scans.

Adaptive Enhancement Technique for Cancerous Lung Nodule in Computed Tomography Images

  • AbuBaker, Ayman A
International Journal of Engineering and Technology 2016 Journal Article, cited 1 times
Website
Diagnosis the Computed Tomography Images (CT-Images) may take a lot of time by the radiologist. This will increase the radiologist fatigue and may miss some of the cancerous lung nodule lesions. Therefore, an adaptive local enhancement Computer Aided Diagnosis (CAD) system is proposed. The proposed technique is design to enhance the suspicious cancerous regions in the CT-Images. The visual characteristics of the cancerous lung nodules in the CT-Images was the main criteria in designing this technique. The new approach is divided into two phases, pre-processing phase and image enhancement phase. The image noise reduction, thresholding process, and extraction the lung regions are considered as a pre-processing phase. Whereas, the new adaptive local enhancement method for the CTImages were implemented as a second phase. The proposed algorithm is tested and evaluated on 42 normal and cancerous lung nodule CT-Images. As a result, this new approach can efficiently enhance the cancerous lung nodules by 25% comparing with the original images.

Automated lung tumor detection and diagnosis in CT Scans using texture feature analysis and SVM

  • Adams, Tim
  • Dörpinghaus, Jens
  • Jacobs, Marc
  • Steinhage, Volker
Communication Papers of the Federated Conference on Computer Science and Information Systems 2018 Journal Article, cited 0 times
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Defining a Radiomic Response Phenotype: A Pilot Study using targeted therapy in NSCLC

  • Aerts, Hugo JWL
  • Grossmann, Patrick
  • Tan, Yongqiang
  • Oxnard, Geoffrey G
  • Rizvi, Naiyer
  • Schwartz, Lawrence H
  • Zhao, Binsheng
Sci RepScientific reports 2016 Journal Article, cited 40 times
Website
Medical imaging plays a fundamental role in oncology and drug development, by providing a non-invasive method to visualize tumor phenotype. Radiomics can quantify this phenotype comprehensively by applying image-characterization algorithms, and may provide important information beyond tumor size or burden. In this study, we investigated if radiomics can identify a gefitinib response-phenotype, studying high-resolution computed-tomography (CT) imaging of forty-seven patients with early-stage non-small cell lung cancer before and after three weeks of therapy. On the baseline-scan, radiomic-feature Laws-Energy was significantly predictive for EGFR-mutation status (AUC = 0.67, p = 0.03), while volume (AUC = 0.59, p = 0.27) and diameter (AUC = 0.56, p = 0.46) were not. Although no features were predictive on the post-treatment scan (p > 0.08), the change in features between the two scans was strongly predictive (significant feature AUC-range = 0.74-0.91). A technical validation revealed that the associated features were also highly stable for test-retest (mean +/- std: ICC = 0.96 +/- 0.06). This pilot study shows that radiomic data before treatment is able to predict mutation status and associated gefitinib response non-invasively, demonstrating the potential of radiomics-based phenotyping to improve the stratification and response assessment between tyrosine kinase inhibitors (TKIs) sensitive and resistant patient populations.

Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach

  • Aerts, H. J.
  • Velazquez, E. R.
  • Leijenaar, R. T.
  • Parmar, C.
  • Grossmann, P.
  • Cavalho, S.
  • Bussink, J.
  • Monshouwer, R.
  • Haibe-Kains, B.
  • Rietveld, D.
  • Hoebers, F.
  • Rietbergen, M. M.
  • Leemans, C. R.
  • Dekker, A.
  • Quackenbush, J.
  • Gillies, R. J.
  • Lambin, P.
2014 Journal Article, cited 1029 times
Website
Human cancers exhibit strong phenotypic differences that can be visualized noninvasively by medical imaging. Radiomics refers to the comprehensive quantification of tumour phenotypes by applying a large number of quantitative image features. Here we present a radiomic analysis of 440 features quantifying tumour image intensity, shape and texture, which are extracted from computed tomography data of 1,019 patients with lung or head-and-neck cancer. We find that a large number of radiomic features have prognostic power in independent data sets of lung and head-and-neck cancer patients, many of which were not identified as significant before. Radiogenomics analysis reveals that a prognostic radiomic signature, capturing intratumour heterogeneity, is associated with underlying gene-expression patterns. These data suggest that radiomics identifies a general prognostic phenotype existing in both lung and head-and-neck cancer. This may have a clinical impact as imaging is routinely used in clinical practice, providing an unprecedented opportunity to improve decision-support in cancer treatment at low cost.

3D-MCN: A 3D Multi-scale Capsule Network for Lung Nodule Malignancy Prediction

  • Afshar, Parnian
  • Oikonomou, Anastasia
  • Naderkhani, Farnoosh
  • Tyrrell, Pascal N
  • Plataniotis, Konstantinos N
  • Farahani, Keyvan
  • Mohammadi, Arash
2020 Journal Article, cited 1 times
Website
Despite the advances in automatic lung cancer malignancy prediction, achieving high accuracy remains challenging. Existing solutions are mostly based on Convolutional Neural Networks (CNNs), which require a large amount of training data. Most of the developed CNN models are based only on the main nodule region, without considering the surrounding tissues. Obtaining high sensitivity is challenging with lung nodule malignancy prediction. Moreover, the interpretability of the proposed techniques should be a consideration when the end goal is to utilize the model in a clinical setting. Capsule networks (CapsNets) are new and revolutionary machine learning architectures proposed to overcome shortcomings of CNNs. Capitalizing on the success of CapsNet in biomedical domains, we propose a novel model for lung tumor malignancy prediction. The proposed framework, referred to as the 3D Multi-scale Capsule Network (3D-MCN), is uniquely designed to benefit from: (i) 3D inputs, providing information about the nodule in 3D; (ii) Multi-scale input, capturing the nodule's local features, as well as the characteristics of the surrounding tissues, and; (iii) CapsNet-based design, being capable of dealing with a small number of training samples. The proposed 3D-MCN architecture predicted lung nodule malignancy with a high accuracy of 93.12%, sensitivity of 94.94%, area under the curve (AUC) of 0.9641, and specificity of 90% when tested on the LIDC-IDRI dataset. When classifying patients as having a malignant condition (i.e., at least one malignant nodule is detected) or not, the proposed model achieved an accuracy of 83%, and a sensitivity and specificity of 84% and 81% respectively.

An Augmentation in the Diagnostic Potency of Breast Cancer through A Deep Learning Cloud-Based AI Framework to Compute Tumor Malignancy & Risk

  • Agarwal, O
International Research Journal of Innovations in Engineering and Technology (IRJIET) 2019 Journal Article, cited 0 times
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This research project focuses on developing a web-based multi-platform solution for augmenting prognostic strategies to diagnose breast cancer (BC), from a variety of different tests, including histology, mammography, cytopathology, and fine-needle aspiration cytology, all inan automated fashion. The respective application utilizes tensor-based data representations and deep learning architectural algorithms, to produce optimized models for the prediction of novel instances against each of these medical tests. This system has been designed in a way that all of its computation can be integrated seamlessly into a clinical setting, without posing any disruption to a clinician’s productivity or workflow, but rather an enhancement of their capabilities. This software can make the diagnostic process automated, standardized, faster, and even more accurate than current benchmarks achieved by both pathologists, and radiologists, which makes it invaluable from a clinical standpoint to make well-informed diagnostic decisions with nominal resources.

Automatic mass detection in mammograms using deep convolutional neural networks

  • Agarwal, Richa
  • Diaz, Oliver
  • Lladó, Xavier
  • Yap, Moi Hoon
  • Martí, Robert
Journal of Medical Imaging 2019 Journal Article, cited 0 times
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With recent advances in the field of deep learning, the use of convolutional neural networks (CNNs) in medical imaging has become very encouraging. The aim of our paper is to propose a patch-based CNN method for automated mass detection in full-field digital mammograms (FFDM). In addition to evaluating CNNs pretrained with the ImageNet dataset, we investigate the use of transfer learning for a particular domain adaptation. First, the CNN is trained using a large public database of digitized mammograms (CBIS-DDSM dataset), and then the model is transferred and tested onto the smaller database of digital mammograms (INbreast dataset). We evaluate three widely used CNNs (VGG16, ResNet50, InceptionV3) and show that the InceptionV3 obtains the best performance for classifying the mass and nonmass breast region for CBIS-DDSM. We further show the benefit of domain adaptation between the CBIS-DDSM (digitized) and INbreast (digital) datasets using the InceptionV3 CNN. Mass detection evaluation follows a fivefold cross-validation strategy using free-response operating characteristic curves. Results show that the transfer learning from CBIS-DDSM obtains a substantially higher performance with the best true positive rate (TPR) of 0.98 0.02 at 1.67 false positives per image (FPI), compared with transfer learning from ImageNet with TPR of 0.91 0.07 at 2.1 FPI. In addition, the proposed framework improves upon mass detection results described in the literature on the INbreast database, in terms of both TPR and FPI.

Patient-Wise Versus Nodule-Wise Classification of Annotated Pulmonary Nodules using Pathologically Confirmed Cases

  • Aggarwal, Preeti
  • Vig, Renu
  • Sardana, HK
Journal of Computers 2013 Journal Article, cited 5 times
Website
This paper presents a novel framework for combining well known shape, texture, size and resolution informatics descriptor of solitary pulmonary nodules (SPNs) detected using CT scan. The proposed methodology evaluates the performance of classifier in differentiating benign, malignant as well as metastasis SPNs with 246 chests CT scan of patients. Both patient-wise as well as nodule-wise available diagnostic report of 80 patients was used in differentiating the SPNs and the results were compared. For patient-wise data, generated a model with efficiency of 62.55% with labeled nodules and using semi-supervised approach, labels of rest of the unknown nodules were predicted and finally classification accuracy of 82.32% is achieved with all labeled nodules. For nodule-wise data, ground truth database of labeled nodules is expanded from a very small ground truth using content based image retrieval (CBIR) method and achieved a precision of 98%. Proposed methodology not only avoids unnecessary biopsies but also efficiently label unknown nodules using pre-diagnosed cases which can certainly help the physicians in diagnosis.

Automatic lung segmentation in low-dose chest CT scans using convolutional deep and wide network (CDWN)

  • Agnes, S Akila
  • Anitha, J
  • Peter, J Dinesh
Neural Computing and Applications 2018 Journal Article, cited 0 times
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Adaptive Multi-Column Deep Neural Networks with Application to Robust Image Denoising

  • Agostinelli, Forest
  • Anderson, Michael R
  • Lee, Honglak
2013 Conference Proceedings, cited 118 times
Website
Stacked sparse denoising auto-encoders (SSDAs) have recently been shown to be successful at removing noise from corrupted images. However, like most denoising techniques, the SSDA is not robust to variation in noise types beyond what it has seen during training. We present the multi-column stacked sparse denoising autoencoder, a novel technique of combining multiple SSDAs into a multi-column SSDA (MC-SSDA) by combining the outputs of each SSDA. We eliminate the need to determine the type of noise, let alone its statistics, at test time. We show that good denoising performance can be achieved with a single system on a variety of different noise types, including ones not seen in the training set. Additionally, we experimentally demonstrate the efficacy of MC-SSDA denoising by achieving MNIST digit error rates on denoised images at close to that of the uncorrupted images.

Assessment of the global noise algorithm for automatic noise measurement in head CT examinations

  • Ahmad, M.
  • Tan, D.
  • Marisetty, S.
Med Phys 2021 Journal Article, cited 0 times
Website
PURPOSE: The global noise (GN) algorithm has been previously introduced as a method for automatic noise measurement in clinical CT images. The accuracy of the GN algorithm has been assessed in abdomen CT examinations, but not in any other body part until now. This work assesses the GN algorithm accuracy in automatic noise measurement in head CT examinations. METHODS: A publicly available image dataset of 99 head CT examinations was used to evaluate the accuracy of the GN algorithm in comparison to reference noise values. Reference noise values were acquired using a manual noise measurement procedure. The procedure used a consistent instruction protocol and multiple observers to mitigate the influence of intra- and interobserver variation, resulting in precise reference values. Optimal GN algorithm parameter values were determined. The GN algorithm accuracy and the corresponding statistical confidence interval were determined. The GN measurements were compared across the six different scan protocols used in this dataset. The correlation of GN to patient head size was also assessed using a linear regression model, and the CT scanner's X-ray beam quality was inferred from the model fit parameters. RESULTS: Across all head CT examinations in the dataset, the range of reference noise was 2.9-10.2 HU. A precision of +/-0.33 HU was achieved in the reference noise measurements. After optimization, the GN algorithm had a RMS error 0.34 HU corresponding to a percent RMS error of 6.6%. The GN algorithm had a bias of +3.9%. Statistically significant differences in GN were detected in 11 out of the 15 different pairs of scan protocols. The GN measurements were correlated with head size with a statistically significant regression slope parameter (p < 10(-7) ). The CT scanner X-ray beam quality estimated from the slope parameter was 3.5 cm water HVL (2.8-4.8 cm 95% CI). CONCLUSION: The GN algorithm was validated for application in head CT examinations. The GN algorithm was accurate in comparison to reference manual measurement, with errors comparable to interobserver variation in manual measurement. The GN algorithm can detect noise differences in examinations performed on different scanner models or using different scan protocols. The trend in GN across patients of different head sizes closely follows that predicted by a physical model of X-ray attenuation.

Tumor Lesion Segmentation from 3D PET Using a Machine Learning Driven Active Surface

  • Ahmadvand, Payam
  • Duggan, Nóirín
  • Bénard, François
  • Hamarneh, Ghassan
2016 Conference Proceedings, cited 4 times
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Increased robustness in reference region model analysis of DCE MRI using two‐step constrained approaches

  • Ahmed, Zaki
  • Levesque, Ives R
Magnetic Resonance in Medicine 2016 Journal Article, cited 1 times
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An extended reference region model for DCE‐MRI that accounts for plasma volume

  • Ahmed, Zaki
  • Levesque, Ives R
NMR in Biomedicine 2018 Journal Article, cited 0 times
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Pharmacokinetic modeling of dynamic contrast-enhanced MRI using a reference region and input function tail

  • Ahmed, Z.
  • Levesque, I. R.
Magn Reson Med 2019 Journal Article, cited 0 times
Website
PURPOSE: Quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI) requires an arterial input function (AIF) which is difficult to measure. We propose the reference region and input function tail (RRIFT) approach which uses a reference tissue and the washout portion of the AIF. METHODS: RRIFT was evaluated in simulations with 100 parameter combinations at various temporal resolutions (5-30 s) and noise levels (sigma = 0.01-0.05 mM). RRIFT was compared against the extended Tofts model (ETM) in 8 studies from patients with glioblastoma multiforme. Two versions of RRIFT were evaluated: one using measured patient-specific AIF tails, and another assuming a literature-based AIF tail. RESULTS: RRIFT estimated the transfer constant K trans and interstitial volume v e with median errors within 20% across all simulations. RRIFT was more accurate and precise than the ETM at temporal resolutions slower than 10 s. The percentage error of K trans had a median and interquartile range of -9 +/- 45% with the ETM and -2 +/- 17% with RRIFT at a temporal resolution of 30 s under noiseless conditions. RRIFT was in excellent agreement with the ETM in vivo, with concordance correlation coefficients (CCC) of 0.95 for K trans , 0.96 for v e , and 0.73 for the plasma volume v p using a measured AIF tail. With the literature-based AIF tail, the CCC was 0.89 for K trans , 0.93 for v e and 0.78 for v p . CONCLUSIONS: Quantitative DCE-MRI analysis using the input function tail and a reference tissue yields absolute kinetic parameters with the RRIFT method. This approach was viable in simulation and in vivo for temporal resolutions as low as 30 s.

Pharmacokinetic modeling of dynamic contrast‐enhanced MRI using a reference region and input function tail

  • Ahmed, Zaki
  • Levesque, Ives R
Magnetic Resonance in Medicine 2020 Journal Article, cited 0 times
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Automated and Manual Quantification of Tumour Cellularity in Digital Slides for Tumour Burden Assessment

  • Akbar, S.
  • Peikari, M.
  • Salama, S.
  • Panah, A. Y.
  • Nofech-Mozes, S.
  • Martel, A. L.
2019 Journal Article, cited 3 times
Website
The residual cancer burden index is an important quantitative measure used for assessing treatment response following neoadjuvant therapy for breast cancer. It has shown to be predictive of overall survival and is composed of two key metrics: qualitative assessment of lymph nodes and the percentage of invasive or in situ tumour cellularity (TC) in the tumour bed (TB). Currently, TC is assessed through eye-balling of routine histopathology slides estimating the proportion of tumour cells within the TB. With the advances in production of digitized slides and increasing availability of slide scanners in pathology laboratories, there is potential to measure TC using automated algorithms with greater precision and accuracy. We describe two methods for automated TC scoring: 1) a traditional approach to image analysis development whereby we mimic the pathologists' workflow, and 2) a recent development in artificial intelligence in which features are learned automatically in deep neural networks using image data alone. We show strong agreements between automated and manual analysis of digital slides. Agreements between our trained deep neural networks and experts in this study (0.82) approach the inter-rater agreements between pathologists (0.89). We also reveal properties that are captured when we apply deep neural network to whole slide images, and discuss the potential of using such visualisations to improve upon TC assessment in the future.

Map-Reduce based tipping point scheduler for parallel image processing

  • Akhtar, Mohammad Nishat
  • Saleh, Junita Mohamad
  • Awais, Habib
  • Bakar, Elmi Abu
Expert Systems with Applications 2019 Journal Article, cited 0 times
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Nowadays, Big Data image processing is very much in need due to its proven success in the field of business information system, medical science and social media. However, as the days are passing by, the computation of Big Data images is becoming more complex which ultimately results in complex resource management and higher task execution time. Researchers have been using a combination of CPU and GPU based computing to cut down the execution time, however, when it comes to scaling of compute nodes, then the combination of CPU and GPU based computing still remains a challenge due to the high communication cost factor. In order to tackle this issue, the Map-Reduce framework has come out to be a viable option as its workflow optimization could be enhanced by changing its underlying job scheduling mechanism. This paper presents a comparative study of job scheduling algorithms which could be deployed over various Big Data based image processing application and also proposes a tipping point scheduling algorithm to optimize the workflow for job execution on multiple nodes. The evaluation of the proposed scheduling algorithm is done by implementing parallel image segmentation algorithm to detect lung tumor for up to 3GB size of image dataset. In terms of performance comprising of task execution time and throughput, the proposed tipping point scheduler has come out to be the best scheduler followed by the Map-Reduce based Fair scheduler. The proposed tipping point scheduler is 1.14 times better than Map-Reduce based Fair scheduler and 1.33 times better than Map-Reduced based FIFO scheduler in terms of task execution time and throughput. In terms of speedup comparison between single node and multiple nodes, the proposed tipping point scheduler attained a speedup of 4.5 X for multi-node architecture. Keywords: Job scheduler; Workflow optimization; Map-Reduce; Tipping point scheduler; Parallel image segmentation; Lung tumor

A review of lung cancer screening and the role of computer-aided detection

  • Al Mohammad, B
  • Brennan, PC
  • Mello-Thoms, C
Clinical Radiology 2017 Journal Article, cited 23 times
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Radiologist performance in the detection of lung cancer using CT

  • Al Mohammad, B
  • Hillis, SL
  • Reed, W
  • Alakhras, M
  • Brennan, PC
Clinical Radiology 2019 Journal Article, cited 2 times
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Breast Cancer Diagnostic System Based on MR images Using KPCA-Wavelet Transform and Support Vector Machine

  • AL-Dabagh, Mustafa Zuhaer
  • AL-Mukhtar, Firas H
IJAERS 2017 Journal Article, cited 0 times
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A Novel Approach to Improving Brain Image Classification Using Mutual Information-Accelerated Singular Value Decomposition

  • Al-Saffar, Zahraa A
  • Yildirim, Tülay
IEEE Access 2020 Journal Article, cited 0 times
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Quantitative assessment of colorectal morphology: Implications for robotic colonoscopy

  • Alazmani, A
  • Hood, A
  • Jayne, D
  • Neville, A
  • Culmer, P
Medical engineering & physics 2016 Journal Article, cited 11 times
Website
This paper presents a method of characterizing the distribution of colorectal morphometrics. It uses three-dimensional region growing and topological thinning algorithms to determine and visualize the luminal volume and centreline of the colon, respectively. Total and segmental lengths, diameters, volumes, and tortuosity angles were then quantified. The effects of body orientations on these parameters were also examined. Variations in total length were predominately due to differences in the transverse colon and sigmoid segments, and did not significantly differ between body orientations. The diameter of the proximal colon was significantly larger than the distal colon, with the largest value at the ascending and cecum segments. The volume of the transverse colon was significantly the largest, while those of the descending colon and rectum were the smallest. The prone position showed a higher frequency of high angles and consequently found to be more torturous than the supine position. This study yielded a method for complete segmental measurements of healthy colorectal anatomy and its tortuosity. The transverse and sigmoid colons were the major determinant in tortuosity and morphometrics between body orientations. Quantitative understanding of these parameters may potentially help to facilitate colonoscopy techniques, accuracy of polyp spatial distribution detection, and design of novel endoscopic devices.

Deep learning for segmentation of brain tumors: Impact of cross-institutional training and testing

  • AlBadawy, E. A.
  • Saha, A.
  • Mazurowski, M. A.
Med Phys 2018 Journal Article, cited 5 times
Website
BACKGROUND AND PURPOSE: Convolutional neural networks (CNNs) are commonly used for segmentation of brain tumors. In this work, we assess the effect of cross-institutional training on the performance of CNNs. METHODS: We selected 44 glioblastoma (GBM) patients from two institutions in The Cancer Imaging Archive dataset. The images were manually annotated by outlining each tumor component to form ground truth. To automatically segment the tumors in each patient, we trained three CNNs: (a) one using data for patients from the same institution as the test data, (b) one using data for the patients from the other institution and (c) one using data for the patients from both of the institutions. The performance of the trained models was evaluated using Dice similarity coefficients as well as Average Hausdorff Distance between the ground truth and automatic segmentations. The 10-fold cross-validation scheme was used to compare the performance of different approaches. RESULTS: Performance of the model significantly decreased (P < 0.0001) when it was trained on data from a different institution (dice coefficients: 0.68 +/- 0.19 and 0.59 +/- 0.19) as compared to training with data from the same institution (dice coefficients: 0.72 +/- 0.17 and 0.76 +/- 0.12). This trend persisted for segmentation of the entire tumor as well as its individual components. CONCLUSIONS: There is a very strong effect of selecting data for training on performance of CNNs in a multi-institutional setting. Determination of the reasons behind this effect requires additional comprehensive investigation.

Self-organizing Approach to Learn a Level-set Function for Object Segmentation in Complex Background Environments

  • Albalooshi, Fatema A
2015 Thesis, cited 0 times
Website
Boundary extraction for object region segmentation is one of the most challenging tasks in image processing and computer vision areas. The complexity of large variations in the appearance of the object and the background in a typical image causes the performance degradation of existing segmentation algorithms. One of the goals of computer vision studies is to produce algorithms to segment object regions to produce accurate object boundaries that can be utilized in feature extraction and classification. This dissertation research considers the incorporation of prior knowledge of intensity/color of objects of interest within segmentation framework to enhance the performance of object region and boundary extraction of targets in unconstrained environments. The information about intensity/color of object of interest is taken from small patches as seeds that are fed to learn a neural network. The main challenge is accounting for the projection transformation between the limited amount of prior information and the appearance of the real object of interest in the testing data. We address this problem by the use of a Self-organizing Map (SOM) which is an unsupervised learning neural network. The segmentation process is achieved by the construction of a local fitted image level-set cost function, in which, the dynamic variable is a Best Matching Unit (BMU) coming from the SOM map. The proposed method is demonstrated on the PASCAL 2011 challenging dataset, in which, images contain objects with variations of illuminations, shadows, occlusions and clutter. In addition, our method is tested on different types of imagery including thermal, hyperspectral, and medical imagery. Metrics illustrate the effectiveness and accuracy of the proposed algorithm in improving the efficiency of boundary extraction and object region detection. In order to reduce computational time, a lattice Boltzmann Method (LBM) convergence criteria is used along with the proposed self-organized active contour model for producing faster and effective segmentation. The lattice Boltzmann method is utilized to evolve the level-set function rapidly and terminate the evolution of the curve at the most optimum region. Experiments performed on our test datasets show promising results in terms of time and quality of the segmentation when compared to other state-of-the-art learning-based active contour model approaches. Our method is more than 53% faster than other state-of-the-art methods. Research is in progress to employ Time Adaptive Self- Organizing Map (TASOM) for improved segmentation and utilize the parallelization property of the LBM to achieve real-time segmentation.

Multi-modal Multi-temporal Brain Tumor Segmentation, Growth Analysis and Texture-based Classification

  • Alberts, Esther
2019 Thesis, cited 0 times
Website
Brain tumor analysis is an active field of research, which has received a lot of attention from both the medical and the technical communities in the past decades. The purpose of this thesis is to investigate brain tumor segmentation, growth analysis and tumor classification based on multi-modal magnetic resonance (MR) image datasets of low- and high-grade glioma making use of computer vision and machine learning methodologies. Brain tumor segmentation involves the delineation of tumorous structures, such as edema, active tumor and necrotic tumor core, and healthy brain tissues, often categorized in gray matter, white matter and cerebro-spinal fluid. Deep learning frameworks have proven to be among the most accurate brain tumor segmentation techniques, performing particularly well when large accurately annotated image datasets are available. A first project is designed to build a more flexible model, which allows for intuitive semi-automated user-interaction, is less dependent on training data, and can handle missing MR modalities. The framework is based on a Bayesian network with hidden variables optimized by the expectation-maximization algorithm, and is tailored to handle non-Gaussian multivariate distributions using the concept of Gaussian copulas. To generate reliable priors for the generative probabilistic model and to spatially regularize the segmentation results, it is extended with an initialization and a post-processing module, both based on supervoxels classified by random forests. Brain tumor segmentation allows to assess tumor volumetry over time, which is important to identify disease progression (tumor regrowth) after therapy. In a second project, a dataset of temporal MR sequences is analyzed. To that end, brain tumor segmentation and brain tumor growth assessment are unified within a single framework using a conditional random field (CRF). The CRF extends over the temporal patient datasets and includes directed links with infinite weight in order to incorporate growth or shrinkage constraints. The model is shown to obtain temporally coherent tumor segmentation and aids in estimating the likelihood of disease progression after therapy. Recent studies classify brain tumors based on their genotypic parameters, which are reported to have an important impact on the prognosis and the therapy of patients. A third project is aimed to investigate whether the genetic profile of glioma can be predicted based on the MR images only, which would eliminate the need to take biopsies. A multi-modal medical image classification framework is built, classifying glioma in three genetic classes based on DNA methylation status. The framework makes use of short local image descriptors as well as deep-learned features acquired by denoising auto-encoders to generate meaningful image features. The framework is successfully validated and shown to obtain high accuracies even though the same image-based classification task is hardly possible for medical experts.

Automatic intensity windowing of mammographic images based on a perceptual metric

  • Albiol, Alberto
  • Corbi, Alberto
  • Albiol, Francisco
Medical Physics 2017 Journal Article, cited 0 times
Website
PURPOSE: Initial auto-adjustment of the window level WL and width WW applied to mammographic images. The proposed intensity windowing (IW) method is based on the maximization of the mutual information (MI) between a perceptual decomposition of the original 12-bit sources and their screen displayed 8-bit version. Besides zoom, color inversion and panning operations, IW is the most commonly performed task in daily screening and has a direct impact on diagnosis and the time involved in the process. METHODS: The authors present a human visual system and perception-based algorithm named GRAIL (Gabor-relying adjustment of image levels). GRAIL initially measures a mammogram's quality based on the MI between the original instance and its Gabor-filtered derivations. From this point on, the algorithm performs an automatic intensity windowing process that outputs the WL/WW that best displays each mammogram for screening. GRAIL starts with the default, high contrast, wide dynamic range 12-bit data, and then maximizes the graphical information presented in ordinary 8-bit displays. Tests have been carried out with several mammogram databases. They comprise correlations and an ANOVA analysis with the manual IW levels established by a group of radiologists. A complete MATLAB implementation of GRAIL is available at https://github.com/TheAnswerIsFortyTwo/GRAIL. RESULTS: Auto-leveled images show superior quality both perceptually and objectively compared to their full intensity range and compared to the application of other common methods like global contrast stretching (GCS). The correlations between the human determined intensity values and the ones estimated by our method surpass that of GCS. The ANOVA analysis with the upper intensity thresholds also reveals a similar outcome. GRAIL has also proven to specially perform better with images that contain micro-calcifications and/or foreign X-ray-opaque elements and with healthy BI-RADS A-type mammograms. It can also speed up the initial screening time by a mean of 4.5 s per image. CONCLUSIONS: A novel methodology is introduced that enables a quality-driven balancing of the WL/WW of mammographic images. This correction seeks the representation that maximizes the amount of graphical information contained in each image. The presented technique can contribute to the diagnosis and the overall efficiency of the breast screening session by suggesting, at the beginning, an optimal and customized windowing setting for each mammogram.

Semi-automatic classification of prostate cancer on multi-parametric MR imaging using a multi-channel 3D convolutional neural network

  • Aldoj, Nader
  • Lukas, Steffen
  • Dewey, Marc
  • Penzkofer, Tobias
Eur Radiol 2019 Journal Article, cited 1 times
Website
OBJECTIVE: To present a deep learning-based approach for semi-automatic prostate cancer classification based on multi-parametric magnetic resonance (MR) imaging using a 3D convolutional neural network (CNN). METHODS: Two hundred patients with a total of 318 lesions for which histological correlation was available were analyzed. A novel CNN was designed, trained, and validated using different combinations of distinct MRI sequences as input (e.g., T2-weighted, apparent diffusion coefficient (ADC), diffusion-weighted images, and K-trans) and the effect of different sequences on the network's performance was tested and discussed. The particular choice of modeling approach was justified by testing all relevant data combinations. The model was trained and validated using eightfold cross-validation. RESULTS: In terms of detection of significant prostate cancer defined by biopsy results as the reference standard, the 3D CNN achieved an area under the curve (AUC) of the receiver operating characteristics ranging from 0.89 (88.6% and 90.0% for sensitivity and specificity respectively) to 0.91 (81.2% and 90.5% for sensitivity and specificity respectively) with an average AUC of 0.897 for the ADC, DWI, and K-trans input combination. The other combinations scored less in terms of overall performance and average AUC, where the difference in performance was significant with a p value of 0.02 when using T2w and K-trans; and 0.00025 when using T2w, ADC, and DWI. Prostate cancer classification performance is thus comparable to that reported for experienced radiologists using the prostate imaging reporting and data system (PI-RADS). Lesion size and largest diameter had no effect on the network's performance. CONCLUSION: The diagnostic performance of the 3D CNN in detecting clinically significant prostate cancer is characterized by a good AUC and sensitivity and high specificity. KEY POINTS: * Prostate cancer classification using a deep learning model is feasible and it allows direct processing of MR sequences without prior lesion segmentation. * Prostate cancer classification performance as measured by AUC is comparable to that of an experienced radiologist. * Perfusion MR images (K-trans), followed by DWI and ADC, have the highest effect on the overall performance; whereas T2w images show hardly any improvement.

Semi-automatic classification of prostate cancer on multi-parametric MR imaging using a multi-channel 3D convolutional neural network

  • Aldoj, Nader
  • Lukas, Steffen
  • Dewey, Marc
  • Penzkofer, Tobias
European Radiology 2020 Journal Article, cited 1 times
Website

Radiogenomics in renal cell carcinoma

  • Alessandrino, Francesco
  • Shinagare, Atul B
  • Bossé, Dominick
  • Choueiri, Toni K
  • Krajewski, Katherine M
Abdominal Radiology 2018 Journal Article, cited 0 times
Website

Automated apparent diffusion coefficient analysis for genotype prediction in lower grade glioma: association with the T2-FLAIR mismatch sign

  • Aliotta, E.
  • Dutta, S. W.
  • Feng, X.
  • Tustison, N. J.
  • Batchala, P. P.
  • Schiff, D.
  • Lopes, M. B.
  • Jain, R.
  • Druzgal, T. J.
  • Mukherjee, S.
  • Patel, S. H.
J Neurooncol 2020 Journal Article, cited 0 times
Website
PURPOSE: The prognosis of lower grade glioma (LGG) patients depends (in large part) on both isocitrate dehydrogenase (IDH) gene mutation and chromosome 1p/19q codeletion status. IDH-mutant LGG without 1p/19q codeletion (IDHmut-Noncodel) often exhibit a unique imaging appearance that includes high apparent diffusion coefficient (ADC) values not observed in other subtypes. The purpose of this study was to develop an ADC analysis-based approach that can automatically identify IDHmut-Noncodel LGG. METHODS: Whole-tumor ADC metrics, including fractional tumor volume with ADC > 1.5 x 10(-3)mm(2)/s (VADC>1.5), were used to identify IDHmut-Noncodel LGG in a cohort of N = 134 patients. Optimal threshold values determined in this dataset were then validated using an external dataset containing N = 93 cases collected from The Cancer Imaging Archive. Classifications were also compared with radiologist-identified T2-FLAIR mismatch sign and evaluated concurrently to identify added value from a combined approach. RESULTS: VADC>1.5 classified IDHmut-Noncodel LGG in the internal cohort with an area under the curve (AUC) of 0.80. An optimal threshold value of 0.35 led to sensitivity/specificity = 0.57/0.93. Classification performance was similar in the validation cohort, with VADC>1.5 >/= 0.35 achieving sensitivity/specificity = 0.57/0.91 (AUC = 0.81). Across both groups, 37 cases exhibited positive T2-FLAIR mismatch sign-all of which were IDHmut-Noncodel. Of these, 32/37 (86%) also exhibited VADC>1.5 >/= 0.35, as did 23 additional IDHmut-Noncodel cases which were negative for T2-FLAIR mismatch sign. CONCLUSION: Tumor subregions with high ADC were a robust indicator of IDHmut-Noncodel LGG, with VADC>1.5 achieving > 90% classification specificity in both internal and validation cohorts. VADC>1.5 exhibited strong concordance with the T2-FLAIR mismatch sign and the combination of both parameters improved sensitivity in detecting IDHmut-Noncodel LGG.

Challenges in predicting glioma survival time in multi-modal deep networks

  • Abdulrhman Aljouie
  • Yunzhe Xue
  • Meiyan Xie
  • Uman Roshan
2020 Conference Paper, cited 0 times
Website
Prediction of cancer survival time is of considerable interest in medicine as it leads to better patient care and reduces health care costs. In this study, we propose a multi-path multimodal neural network that predicts Glioblastoma Multiforme (GBM) survival time at the 14 months threshold. We obtained image, gene expression, and SNP variants from whole-exome sequences all from the The Cancer Genome Atlas portal for a total of 126 patients. We perform a 10-fold cross-validation experiment on each of the data sources separately as well as the model with all data combined. From post-contrast Tl MRI data, we used 3D scans and 2D slices that we selected manually to show the tumor region. We find that the model with 2D MRI slices and genomic data combined gives the highest accuracies over individual sources but by a modest margin. We see considerable variation in accuracies across the 10 folds and that our model achieves 100% accuracy on the training data but lags behind in test accuracy. With dropout our training accuracy falls considerably. This shows that predicting glioma survival time is a challenging task but it is unclear if this is also a symptom of insufficient data. A clear direction here is to augment our data that we plan to explore with generative models. Overall we present a novel multi-modal network that incorporates SNP, gene expression, and MRI image data for glioma survival time prediction.

Versatile Convolutional Networks Applied to Computed Tomography and Magnetic Resonance Image Segmentation

  • Almeida, Gonçalo
  • Tavares, João Manuel R. S.
Journal of Medical Systems 2021 Journal Article, cited 0 times
Website
Medical image segmentation has seen positive developments in recent years but remains challenging with many practical obstacles to overcome. The applications of this task are wide-ranging in many fields of medicine, and used in several imaging modalities which usually require tailored solutions. Deep learning models have gained much attention and have been lately recognized as the most successful for automated segmentation. In this work we show the versatility of this technique by means of a single deep learning architecture capable of successfully performing segmentation on two very different types of imaging: computed tomography and magnetic resonance. The developed model is fully convolutional with an encoder-decoder structure and high-resolution pathways which can process whole three-dimensional volumes at once, and learn directly from the data to find which voxels belong to the regions of interest and localize those against the background. The model was applied to two publicly available datasets achieving equivalent results for both imaging modalities, as well as performing segmentation of different organs in different anatomic regions with comparable success.

Robust Detection of Circles in the Vessel Contours and Application to Local Probability Density Estimation

  • Alvarez, Luis
  • González, Esther
  • Esclarín, Julio
  • Gomez, Luis
  • Alemán-Flores, Miguel
  • Trujillo, Agustín
  • Cuenca, Carmelo
  • Mazorra, Luis
  • Tahoces, Pablo G
  • Carreira, José M
2017 Book Section, cited 3 times
Website

Comparative Analysis of Lossless Image Compression Algorithms based on Different Types of Medical Images

  • Alzahrani, Mona
  • Albinali, Mona
2021 Conference Paper, cited 0 times
Website
In the medical field, there is a demand for highspeed transmission and efficient storage of medical images between healthcare organizations. Therefore, image compression techniques are essential in that field. In this study, we conducted an experimental comparison between two famous lossless algorithms: lossless Discrete Cosine Transform (DCT) and lossless Haar Wavelet Transform (HWT). Covering three different datasets that contain different types of medical images: MRI, CT, and gastrointestinal endoscopic images; with different image formats PNG, JPG and TIF. According to the conducted experiments, in terms of compressed image size and compression ratio, we found that DCT outperforms HWT regarding PNG and TIF format which represent CT-grey and MRI-color images. And regarding JPG format which represents the gastrointestinal endoscopic color images, DCT performs well when grey-scale images are used; where HWT outperforms DCT when color images are used. However, HWT outperforms DCT in compression time regarding all the image types and formats.

Transferable HMM probability matrices in multi‐orientation geometric medical volumes segmentation

  • AlZu'bi, Shadi
  • AlQatawneh, Sokyna
  • ElBes, Mohammad
  • Alsmirat, Mohammad
Concurrency and Computation: Practice and Experience 2019 Journal Article, cited 0 times
Website
Acceptable error rate, low quality assessment, and time complexity are the major problems in image segmentation, which needed to be discovered. A variety of acceleration techniques have been applied and achieve real time results, but still limited in 3D. HMM is one of the best statistical techniques that played a significant rule recently. The problem associated with HMM is time complexity, which has been resolved using different accelerator. In this research, we propose a methodology for transferring HMM matrices from image to another skipping the training time for the rest of the 3D volume. One HMM train is generated and generalized to the whole volume. The concepts behind multi‐orientation geometrical segmentation has been employed here to improve the quality of HMM segmentation. Axial, saggital, and coronal orientations have been considered individually and together to achieve accurate segmentation results in less processing time and superior quality in the detection accuracy.

Imaging Biomarker Ontology (IBO): A Biomedical Ontology to Annotate and Share Imaging Biomarker Data

  • Amdouni, Emna
  • Gibaud, Bernard
Journal on Data Semantics 2018 Journal Article, cited 0 times
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Hybrid Mass Detection in Breast MRI Combining Unsupervised Saliency Analysis and Deep Learning

  • Amit, Guy
  • Hadad, Omer
  • Alpert, Sharon
  • Tlusty, Tal
  • Gur, Yaniv
  • Ben-Ari, Rami
  • Hashoul, Sharbell
2017 Conference Paper, cited 15 times
Website
To interpret a breast MRI study, a radiologist has to examine over 1000 images, and integrate spatial and temporal information from multiple sequences. The automated detection and classification of suspicious lesions can help reduce the workload and improve accuracy. We describe a hybrid mass-detection algorithm that combines unsupervised candidate detection with deep learning-based classification. The detection algorithm first identifies image-salient regions, as well as regions that are cross-salient with respect to the contralateral breast image. We then use a convolutional neural network (CNN) to classify the detected candidates into true-positive and false-positive masses. The network uses a novel multi-channel image representation; this representation encompasses information from the anatomical and kinetic image features, as well as saliency maps. We evaluated our algorithm on a dataset of MRI studies from 171 patients, with 1957 annotated slices of malignant (59%) and benign (41%) masses. Unsupervised saliency-based detection provided a sensitivity of 0.96 with 9.7 false-positive detections per slice. Combined with CNN classification, the number of false positive detections dropped to 0.7 per slice, with 0.85 sensitivity. The multi-channel representation achieved higher classification performance compared to single-channel images. The combination of domain-specific unsupervised methods and general-purpose supervised learning offers advantages for medical imaging applications, and may improve the ability of automated algorithms to assist radiologists.

Breast Cancer Response Prediction in Neoadjuvant Chemotherapy Treatment Based on Texture Analysis

  • Ammar, Mohammed
  • Mahmoudi, Saïd
  • Stylianos, Drisis
Procedia Computer Science 2016 Journal Article, cited 2 times
Website
MRI modality is one of the most usual techniques used for diagnosis and treatment planning of breast cancer. The aim of this study is to prove that texture based feature techniques such as co-occurrence matrix features extracted from MRI images can be used to quantify response of tumor treatment. To this aim, we use a dataset composed of two breast MRI examinations for 9 patients. Three of them were responders and six non responders. The first exam was achieved before the initiation of the treatment (baseline). The later one was done after the first cycle of the chemo treatment (control). A set of selected texture parameters have been selected and calculated for each exam. These selected parameters are: Cluster Shade, dissimilarity, entropy, homogeneity. The p-values estimated for the pathologic complete responders pCR and non pathologic complete responders pNCR patients prove that homogeneity (P-value=0.027) and cluster shade (P-value=0.0013) are the more relevant parameters related to pathologic complete responders pCR.

Medical Image Classification Algorithm Based on Weight Initialization-Sliding Window Fusion Convolutional Neural Network

  • An, Feng-Ping
Complexity 2019 Journal Article, cited 0 times
Website
Due to the complexity of medical images, traditional medical image classification methods have been unable to meet actual application needs. In recent years, the rapid development of deep learning theory has provided a technical approach for solving medical image classification tasks. However, deep learning has the following problems in medical image classification. First, it is impossible to construct a deep learning model hierarchy for medical image properties; second, the network initialization weights of deep learning models are not well optimized. Therefore, this paper starts from the perspective of network optimization and improves the nonlinear modeling ability of the network through optimization methods. A new network weight initialization method is proposed, which alleviates the problem that existing deep learning model initialization is limited by the type of the nonlinear unit adopted and increases the potential of the neural network to handle different visual tasks. Moreover, through an in-depth study of the multicolumn convolutional neural network framework, this paper finds that the number of features and the convolution kernel size at different levels of the convolutional neural network are different. In contrast, the proposed method can construct different convolutional neural network models that adapt better to the characteristics of the medical images of interest and thus can better train the resulting heterogeneous multicolumn convolutional neural networks. Finally, using the adaptive sliding window fusion mechanism proposed in this paper, both methods jointly complete the classification task of medical images. Based on the above ideas, this paper proposes a medical classification algorithm based on a weight initialization/sliding window fusion for multilevel convolutional neural networks. The methods proposed in this study were applied to breast mass, brain tumor tissue, and medical image database classification experiments. The results show that the proposed method not only achieves a higher average accuracy than that of traditional machine learning and other deep learning methods but also is more stable and more robust.

Application of Fuzzy c-means and Neural networks to categorize tumor affected breast MR Images

  • Anand, Shruthi
  • Vinod, Viji
  • Rampure, Anand
International Journal of Applied Engineering Research 2015 Journal Article, cited 4 times
Website

Imaging Genomics in Glioblastoma Multiforme: A Predictive Tool for Patients Prognosis, Survival, and Outcome

  • Anil, Rahul
  • Colen, Rivka R
Magnetic Resonance Imaging Clinics of North America 2016 Journal Article, cited 3 times
Website
The integration of imaging characteristics and genomic data has started a new trend in approach toward management of glioblastoma (GBM). Many ongoing studies are investigating imaging phenotypical signatures that could explain more about the behavior of GBM and its outcome. The discovery of biomarkers has played an adjuvant role in treating and predicting the outcome of patients with GBM. Discovering these imaging phenotypical signatures and dysregulated pathways/genes is needed and required to engineer treatment based on specific GBM manifestations. Characterizing these parameters will establish well-defined criteria so researchers can build on the treatment of GBM through personal medicine.

Lung nodule detection using 3D convolutional neural networks trained on weakly labeled data

  • Anirudh, Rushil
  • Thiagarajan, Jayaraman J
  • Bremer, Timo
  • Kim, Hyojin
2016 Conference Proceedings, cited 33 times
Website

Brain tumour classification using two-tier classifier with adaptive segmentation technique

  • Anitha, V
  • Murugavalli, S
IET Computer VisionIet Comput Vis 2016 Journal Article, cited 46 times
Website
A brain tumour is a mass of tissue that is structured by a gradual addition of anomalous cells and it is important to classify brain tumours from the magnetic resonance imaging (MRI) for treatment. Human investigation is the routine technique for brain MRI tumour detection and tumours classification. Interpretation of images is based on organised and explicit classification of brain MRI and also various techniques have been proposed. Information identified with anatomical structures and potential abnormal tissues which are noteworthy to treat are given by brain tumour segmentation on MRI, the proposed system uses the adaptive pillar K-means algorithm for successful segmentation and the classification methodology is done by the two-tier classification approach. In the proposed system, at first the self-organising map neural network trains the features extracted from the discrete wavelet transform blend wavelets and the resultant filter factors are consequently trained by the K-nearest neighbour and the testing process is also accomplished in two stages. The proposed two-tier classification system classifies the brain tumours in double training process which gives preferable performance over the traditional classification method. The proposed system has been validated with the support of real data sets and the experimental results showed enhanced performance.

Classification of lung adenocarcinoma transcriptome subtypes from pathological images using deep convolutional networks

  • Antonio, Victor Andrew A
  • Ono, Naoaki
  • Saito, Akira
  • Sato, Tetsuo
  • Altaf-Ul-Amin, Md
  • Kanaya, Shigehiko
International Journal of Computer Assisted Radiology and Surgery 2018 Journal Article, cited 0 times
Website
PURPOSE: Convolutional neural networks have become rapidly popular for image recognition and image analysis because of its powerful potential. In this paper, we developed a method for classifying subtypes of lung adenocarcinoma from pathological images using neural network whose that can evaluate phenotypic features from wider area to consider cellular distributions. METHODS: In order to recognize the types of tumors, we need not only to detail features of cells, but also to incorporate statistical distribution of the different types of cells. Variants of autoencoders as building blocks of pre-trained convolutional layers of neural networks are implemented. A sparse deep autoencoder which minimizes local information entropy on the encoding layer is then proposed and applied to images of size [Formula: see text]. We applied this model for feature extraction from pathological images of lung adenocarcinoma, which is comprised of three transcriptome subtypes previously defined by the Cancer Genome Atlas network. Since the tumor tissue is composed of heterogeneous cell populations, recognition of tumor transcriptome subtypes requires more information than local pattern of cells. The parameters extracted using this approach will then be used in multiple reduction stages to perform classification on larger images. RESULTS: We were able to demonstrate that these networks successfully recognize morphological features of lung adenocarcinoma. We also performed classification and reconstruction experiments to compare the outputs of the variants. The results showed that the larger input image that covers a certain area of the tissue is required to recognize transcriptome subtypes. The sparse autoencoder network with [Formula: see text] input provides a 98.9% classification accuracy. CONCLUSION: This study shows the potential of autoencoders as a feature extraction paradigm and paves the way for a whole slide image analysis tool to predict molecular subtypes of tumors from pathological features.

Fast wavelet based image characterization for content based medical image retrieval

  • Anwar, Syed Muhammad
  • Arshad, Fozia
  • Majid, Muhammad
2017 Conference Proceedings, cited 4 times
Website
A large collection of medical images surrounds health care centers and hospitals. Medical images produced by different modalities like magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), and X-rays have increased incredibly with the advent of latest technologies for image acquisition. Retrieving clinical images of interest from these large data sets is a thought-provoking and demanding task. In this paper, a fast wavelet based medical image retrieval system is proposed that can aid physicians in the identification or analysis of medical images. The image signature is calculated using kurtosis and standard deviation as features. A possible use case is when the radiologist has some suspicion on diagnosis and wants further case histories, the acquired clinical images are sent (e.g. MRI images of brain) as a query to the content based medical image retrieval system. The system is tuned to retrieve the top most relevant images to the query. The proposed system is computationally efficient and more accurate in terms of the quality of retrieved images.

Hand-Crafted and Deep Learning-Based Radiomics Models for Recurrence Prediction of Non-Small Cells Lung Cancers

  • Aonpong, Panyanat
  • Iwamoto, Yutaro
  • Wang, Weibin
  • Lin, Lanfen
  • Chen, Yen-Wei
Innovation in Medicine and Healthcare 2020 Journal Article, cited 0 times
Website
This research was created to examine the recurrence of non-small lung cancer (NSCLC) using computed-tomography images (CT-images) to avoid biopsy from patients because the cancer cells may have an uneven distribution which can lead to the investigation mistake. This work presents a comparison of the operations of two different methods: Hand-Crafted Radiomics model and deep learning-based radiomics model using 88 patient samples from open-access dataset of non-small cell lung cancer in The Cancer Imaging Archive (TCIA) Public Access. In Hand-Crafted Radiomics Models, the pattern of NSCLC CT-images was analyzed in various statistics as radiomics features. The radiomics features associated with recurrence are selected through three statistical calculations: LASSO, Chi-2, and ANOVA. Then, those selected radiomics features were processed using different models. In the Deep Learning-based Radiomics Model, the proposed artificial neural network has been used to enhance the recurrence prediction. The Hand-Crafted Radiomics Model with non-selected, Lasso, Chi-2, and ANOVA, give the following results: 76.56% (AUC 0.6361), 76.83% (AUC 0.6375), 78.64% (AUC 0.6778), and 78.17% (AUC 0.6556), respectively, and the Deep Learning-based Radiomic Models, including ResNet50 and DenseNet121 give the following results: 79.00% (AUC 0.6714), and 79.31% (AUC 0.6712), respectively.

Automatic classification of solitary pulmonary nodules in PET/CT imaging employing transfer learning techniques

  • Apostolopoulos, Ioannis D
  • Pintelas, Emmanuel G
  • Livieris, Ioannis E
  • Apostolopoulos, Dimitris J
  • Papathanasiou, Nikolaos D
  • Pintelas, Panagiotis E
  • Panayiotakis, George S
2021 Journal Article, cited 0 times
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End-to-end lung cancer screening with three-dimensional deep learning on low-dose chest computed tomography

  • Ardila, D.
  • Kiraly, A. P.
  • Bharadwaj, S.
  • Choi, B.
  • Reicher, J. J.
  • Peng, L.
  • Tse, D.
  • Etemadi, M.
  • Ye, W.
  • Corrado, G.
  • Naidich, D. P.
  • Shetty, S.
Nat Med 2019 Journal Article, cited 1 times
Website
With an estimated 160,000 deaths in 2018, lung cancer is the most common cause of cancer death in the United States(1). Lung cancer screening using low-dose computed tomography has been shown to reduce mortality by 20-43% and is now included in US screening guidelines(1-6). Existing challenges include inter-grader variability and high false-positive and false-negative rates(7-10). We propose a deep learning algorithm that uses a patient's current and prior computed tomography volumes to predict the risk of lung cancer. Our model achieves a state-of-the-art performance (94.4% area under the curve) on 6,716 National Lung Cancer Screening Trial cases, and performs similarly on an independent clinical validation set of 1,139 cases. We conducted two reader studies. When prior computed tomography imaging was not available, our model outperformed all six radiologists with absolute reductions of 11% in false positives and 5% in false negatives. Where prior computed tomography imaging was available, the model performance was on-par with the same radiologists. This creates an opportunity to optimize the screening process via computer assistance and automation. While the vast majority of patients remain unscreened, we show the potential for deep learning models to increase the accuracy, consistency and adoption of lung cancer screening worldwide.

Potentials of radiomics for cancer diagnosis and treatment in comparison with computer-aided diagnosis

  • Arimura, Hidetaka
  • Soufi, Mazen
  • Ninomiya, Kenta
  • Kamezawa, Hidemi
  • Yamada, Masahiro
Radiological Physics and Technology 2018 Journal Article, cited 0 times
Website
Computer-aided diagnosis (CAD) is a field that is essentially based on pattern recognition that improves the accuracy of a diagnosis made by a physician who takes into account the computer’s “opinion” derived from the quantitative analysis of radiological images. Radiomics is a field based on data science that massively and comprehensively analyzes a large number of medical images to extract a large number of phenotypic features reflecting disease traits, and explores the associations between the features and patients’ prognoses for precision medicine. According to the definitions for both, you may think that radiomics is not a paraphrase of CAD, but you may also think that these definitions are “image manipulation”. However, there are common and different features between the two fields. This review paper elaborates on these common and different features and introduces the potential of radiomics for cancer diagnosis and treatment by comparing it with CAD.

The lung image database consortium (LIDC) and image database resource initiative (IDRI): a completed reference database of lung nodules on CT scans

  • Armato III, Samuel G
  • McLennan, Geoffrey
  • Bidaut, Luc
  • McNitt-Gray, Michael F
  • Meyer, Charles R
  • Reeves, Anthony P
  • Zhao, Binsheng
  • Aberle, Denise R
  • Henschke, Claudia I
  • Hoffman, Eric A
  • Kazerooni, E. A.
  • MacMahon, H.
  • Van Beeke, E. J.
  • Yankelevitz, D.
  • Biancardi, A. M.
  • Bland, P. H.
  • Brown, M. S.
  • Engelmann, R. M.
  • Laderach, G. E.
  • Max, D.
  • Pais, R. C.
  • Qing, D. P.
  • Roberts, R. Y.
  • Smith, A. R.
  • Starkey, A.
  • Batrah, P.
  • Caligiuri, P.
  • Farooqi, A.
  • Gladish, G. W.
  • Jude, C. M.
  • Munden, R. F.
  • Petkovska, I.
  • Quint, L. E.
  • Schwartz, L. H.
  • Sundaram, B.
  • Dodd, L. E.
  • Fenimore, C.
  • Gur, D.
  • Petrick, N.
  • Freymann, J.
  • Kirby, J.
  • Hughes, B.
  • Casteele, A. V.
  • Gupte, S.
  • Sallamm, M.
  • Heath, M. D.
  • Kuhn, M. H.
  • Dharaiya, E.
  • Burns, R.
  • Fryd, D. S.
  • Salganicoff, M.
  • Anand, V.
  • Shreter, U.
  • Vastagh, S.
  • Croft, B. Y.
Medical Physics 2011 Journal Article, cited 546 times
Website
PURPOSE: The development of computer-aided diagnostic (CAD) methods for lung nodule detection, classification, and quantitative assessment can be facilitated through a well-characterized repository of computed tomography (CT) scans. The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI) completed such a database, establishing a publicly available reference for the medical imaging research community. Initiated by the National Cancer Institute (NCI), further advanced by the Foundation for the National Institutes of Health (FNIH), and accompanied by the Food and Drug Administration (FDA) through active participation, this public-private partnership demonstrates the success of a consortium founded on a consensus-based process. METHODS: Seven academic centers and eight medical imaging companies collaborated to identify, address, and resolve challenging organizational, technical, and clinical issues to provide a solid foundation for a robust database. The LIDC/IDRI Database contains 1018 cases, each of which includes images from a clinical thoracic CT scan and an associated XML file that records the results of a two-phase image annotation process performed by four experienced thoracic radiologists. In the initial blinded-read phase, each radiologist independently reviewed each CT scan and marked lesions belonging to one of three categories ("nodule > or =3 mm," "nodule <3 mm," and "non-nodule > or =3 mm"). In the subsequent unblinded-read phase, each radiologist independently reviewed their own marks along with the anonymized marks of the three other radiologists to render a final opinion. The goal of this process was to identify as completely as possible all lung nodules in each CT scan without requiring forced consensus. RESULTS: The Database contains 7371 lesions marked "nodule" by at least one radiologist. 2669 of these lesions were marked "nodule > or =3 mm" by at least one radiologist, of which 928 (34.7%) received such marks from all four radiologists. These 2669 lesions include nodule outlines and subjective nodule characteristic ratings. CONCLUSIONS: The LIDC/IDRI Database is expected to provide an essential medical imaging research resource to spur CAD development, validation, and dissemination in clinical practice.

Collaborative projects

  • Armato, S
  • McNitt-Gray, M
  • Meyer, C
  • Reeves, A
  • Clarke, L
Int J CARS 2012 Journal Article, cited 307 times
Website

Special Section Guest Editorial: LUNGx Challenge for computerized lung nodule classification: reflections and lessons learned

  • Armato, Samuel G
  • Hadjiiski, Lubomir
  • Tourassi, Georgia D
  • Drukker, Karen
  • Giger, Maryellen L
  • Li, Feng
  • Redmond, George
  • Farahani, Keyvan
  • Kirby, Justin S
  • Clarke, Laurence P
Journal of Medical Imaging 2015 Journal Article, cited 20 times
Website
The purpose of this work is to describe the LUNGx Challenge for the computerized classification of lung nodules on diagnostic computed tomography (CT) scans as benign or malignant and report the performance of participants' computerized methods along with that of six radiologists who participated in an observer study performing the same Challenge task on the same dataset. The Challenge provided sets of calibration and testing scans, established a performance assessment process, and created an infrastructure for case dissemination and result submission. Ten groups applied their own methods to 73 lung nodules (37 benign and 36 malignant) that were selected to achieve approximate size matching between the two cohorts. Area under the receiver operating characteristic curve (AUC) values for these methods ranged from 0.50 to 0.68; only three methods performed statistically better than random guessing. The radiologists' AUC values ranged from 0.70 to 0.85; three radiologists performed statistically better than the best-performing computer method. The LUNGx Challenge compared the performance of computerized methods in the task of differentiating benign from malignant lung nodules on CT scans, placed in the context of the performance of radiologists on the same task. The continued public availability of the Challenge cases will provide a valuable resource for the medical imaging research community.

Discovery of pre-therapy 2-deoxy-2-18 F-fluoro-D-glucose positron emission tomography-based radiomics classifiers of survival outcome in non-small-cell lung cancer patients

  • Arshad, Mubarik A
  • Thornton, Andrew
  • Lu, Haonan
  • Tam, Henry
  • Wallitt, Kathryn
  • Rodgers, Nicola
  • Scarsbrook, Andrew
  • McDermott, Garry
  • Cook, Gary J
  • Landau, David
European journal of nuclear medicine and molecular imaging 2018 Journal Article, cited 0 times
Website

Effect of Applying Leakage Correction on rCBV Measurement Derived From DSC-MRI in Enhancing and Nonenhancing Glioma

  • Arzanforoosh, Fatemeh
  • Croal, Paula L.
  • van Garderen, Karin A.
  • Smits, Marion
  • Chappell, Michael A.
  • Warnert, Esther A. H.
Frontiers in Oncology 2021 Journal Article, cited 0 times
Website
Purpose: Relative cerebral blood volume (rCBV) is the most widely used parameter derived from DSC perfusion MR imaging for predicting brain tumor aggressiveness. However, accurate rCBV estimation is challenging in enhancing glioma, because of contrast agent extravasation through a disrupted blood-brain barrier (BBB), and even for nonenhancing glioma with an intact BBB, due to an elevated steady-state contrast agent concentration in the vasculature after first passage. In this study a thorough investigation of the effects of two different leakage correction algorithms on rCBV estimation for enhancing and nonenhancing tumors was conducted. Methods: Two datasets were used retrospectively in this study: 1. A publicly available TCIA dataset (49 patients with 35 enhancing and 14 nonenhancing glioma); 2. A dataset acquired clinically at Erasmus MC (EMC, Rotterdam, NL) (47 patients with 20 enhancing and 27 nonenhancing glial brain lesions). The leakage correction algorithms investigated in this study were: a unidirectional model-based algorithm with flux of contrast agent from the intra- to the extravascular extracellular space (EES); and a bidirectional model-based algorithm additionally including flow from EES to the intravascular space. Results: In enhancing glioma, the estimated average contrast-enhanced tumor rCBV significantly (Bonferroni corrected Wilcoxon Signed Rank Test, p < 0.05) decreased across the patients when applying unidirectional and bidirectional correction: 4.00 ± 2.11 (uncorrected), 3.19 ± 1.65 (unidirectional), and 2.91 ± 1.55 (bidirectional) in TCIA dataset and 2.51 ± 1.3 (uncorrected), 1.72 ± 0.84 (unidirectional), and 1.59 ± 0.9 (bidirectional) in EMC dataset. In nonenhancing glioma, a significant but smaller difference in observed rCBV was found after application of both correction methods used in this study: 1.42 ± 0.60 (uncorrected), 1.28 ± 0.46 (unidirectional), and 1.24 ± 0.37 (bidirectional) in TCIA dataset and 0.91 ± 0.49 (uncorrected), 0.77 ± 0.37 (unidirectional), and 0.67 ± 0.34 (bidirectional) in EMC dataset. Conclusion: Both leakage correction algorithms were found to change rCBV estimation with BBB disruption in enhancing glioma, and to a lesser degree in nonenhancing glioma. Stronger effects were found for bidirectional leakage correction than for unidirectional leakage correction.

Morphological and multi-level geometrical descriptor analysis in CT and MRI volumes for automatic pancreas segmentation

  • Asaturyan, Hykoush
  • Gligorievski, Antonio
  • Villarini, Barbara
Computerized Medical Imaging and Graphics 2019 Journal Article, cited 3 times
Website
Automatic pancreas segmentation in 3D radiological scans is a critical, yet challenging task. As a prerequisite for computer-aided diagnosis (CADx) systems, accurate pancreas segmentation could generate both quantitative and qualitative information towards establishing the severity of a condition, and thus provide additional guidance for therapy planning. Since the pancreas is an organ of high inter-patient anatomical variability, previous segmentation approaches report lower quantitative accuracy scores in comparison to abdominal organs such as the liver or kidneys. This paper presents a novel approach for automatic pancreas segmentation in magnetic resonance imaging (MRI) and computer tomography (CT) scans. This method exploits 3D segmentation that, when coupled with geometrical and morphological characteristics of abdominal tissue, classifies distinct contours in tight pixel-range proximity as “pancreas” or “non-pancreas”. There are three main stages to this approach: (1) identify a major pancreas region and apply contrast enhancement to differentiate between pancreatic and surrounding tissue; (2) perform 3D segmentation via continuous max-flow and min-cuts approach, structured forest edge detection, and a training dataset of annotated pancreata; (3) eliminate non-pancreatic contours from resultant segmentation via morphological operations on area, structure and connectivity between distinct contours. The proposed method is evaluated on a dataset containing 82 CT image volumes, achieving mean Dice Similarity coefficient (DSC) of 79.3 ± 4.4%. Two MRI datasets containing 216 and 132 image volumes are evaluated, achieving mean DSC 79.6 ± 5.7% and 81.6 ± 5.1% respectively. This approach is statistically stable, reflected by lower metrics in standard deviation in comparison to state-of-the-art approaches.

Fusion of CT and MR Liver Images by SURF-Based Registration

  • Aslan, Muhammet Fatih
  • Durdu, Akif
International Journal of Intelligent Systems and Applications in Engineering 2019 Journal Article, cited 3 times
Website

Early survival prediction in non-small cell lung cancer from PET/CT images using an intra-tumor partitioning method.

  • Astaraki, Mehdi
  • Wang, Chunliang
  • Buizza, Giulia
  • Toma-Dasu, Iuliana
  • Lazzeroni, Marta
  • Smedby, Orjan
Physica Medica 2019 Journal Article, cited 0 times
Website
PURPOSE: To explore prognostic and predictive values of a novel quantitative feature set describing intra-tumor heterogeneity in patients with lung cancer treated with concurrent and sequential chemoradiotherapy. METHODS: Longitudinal PET-CT images of 30 patients with non-small cell lung cancer were analysed. To describe tumor cell heterogeneity, the tumors were partitioned into one to ten concentric regions depending on their sizes, and, for each region, the change in average intensity between the two scans was calculated for PET and CT images separately to form the proposed feature set. To validate the prognostic value of the proposed method, radiomics analysis was performed and a combination of the proposed novel feature set and the classic radiomic features was evaluated. A feature selection algorithm was utilized to identify the optimal features, and a linear support vector machine was trained for the task of overall survival prediction in terms of area under the receiver operating characteristic curve (AUROC). RESULTS: The proposed novel feature set was found to be prognostic and even outperformed the radiomics approach with a significant difference (AUROCSALoP=0.90 vs. AUROCradiomic=0.71) when feature selection was not employed, whereas with feature selection, a combination of the novel feature set and radiomics led to the highest prognostic values. CONCLUSION: A novel feature set designed for capturing intra-tumor heterogeneity was introduced. Judging by their prognostic power, the proposed features have a promising potential for early survival prediction.

Multimodal Brain Tumor Segmentation with Normal Appearance Autoencoder

  • Astaraki, Mehdi
  • Wang, Chunliang
  • Carrizo, Gabriel
  • Toma-Dasu, Iuliana
  • Smedby, Örjan
2020 Conference Paper, cited 0 times
Website
We propose a hybrid segmentation pipeline based on the autoencoders’ capability of anomaly detection. To this end, we, first, introduce a new augmentation technique to generate synthetic paired images. Gaining advantage from the paired images, we propose a Normal Appearance Autoencoder (NAA) that is able to remove tumors and thus reconstruct realistic-looking, tumor-free images. After estimating the regions where the abnormalities potentially exist, a segmentation network is guided toward the candidate region. We tested the proposed pipeline on the BraTS 2019 database. The preliminary results indicate that the proposed model improved the segmentation accuracy of brain tumor subregions compared to the U-Net model.

Computer Aided Detection Scheme To Improve The Prognosis Assessment Of Early Stage Lung Cancer Patients

  • Athira, KV
  • Nithin, SS
Computer 2018 Journal Article, cited 0 times
Website
To develop a computer aided detection scheme to predict the stage 1 non-small cell lung cancer recurrence risk in lung cancer patients after surgery. By using chest computed tomography images; that taken before surgery, this system automatically segment the tumor that seen on CT images and extract the tumor related morphological and texture-based image features. We trained a Naïve Bayesian network classifier using six image features and an ANN classifier using two genomic biomarkers, these biomarkers are protein expression of the excision repair cross-complementing 1 gene (ERCC1) & a regulatory subunit of ribonucleotide reductase (RRM1) to predict the cancer recurrence risk, respectively. We developed a new approach that has a high potential to assist doctors in more effectively managing first stage NSCLC patients to reduce the cancer recurrence risk.

Analysis of dual tree M‐band wavelet transform based features for brain image classification

  • Ayalapogu, Ratna Raju
  • Pabboju, Suresh
  • Ramisetty, Rajeswara Rao
Magnetic Resonance in Medicine 2018 Journal Article, cited 1 times
Website

OpenKBP: The open‐access knowledge‐based planning grand challenge and dataset

  • Babier, A.
  • Zhang, B.
  • Mahmood, R.
  • Moore, K. L.
  • Purdie, T. G.
  • McNiven, A. L.
  • Chan, T. C. Y.
Medical Physics 2021 Journal Article, cited 0 times
Website
PURPOSE: To advance fair and consistent comparisons of dose prediction methods for knowledge-based planning (KBP) in radiation therapy research. METHODS: We hosted OpenKBP, a 2020 AAPM Grand Challenge, and challenged participants to develop the best method for predicting the dose of contoured computed tomography (CT) images. The models were evaluated according to two separate scores: (a) dose score, which evaluates the full three-dimensional (3D) dose distributions, and (b) dose-volume histogram (DVH) score, which evaluates a set DVH metrics. We used these scores to quantify the quality of the models based on their out-of-sample predictions. To develop and test their models, participants were given the data of 340 patients who were treated for head-and-neck cancer with radiation therapy. The data were partitioned into training ( n = 200 ), validation ( n = 40 ), and testing ( n = 100 ) datasets. All participants performed training and validation with the corresponding datasets during the first (validation) phase of the Challenge. In the second (testing) phase, the participants used their model on the testing data to quantify the out-of-sample performance, which was hidden from participants and used to determine the final competition ranking. Participants also responded to a survey to summarize their models. RESULTS: The Challenge attracted 195 participants from 28 countries, and 73 of those participants formed 44 teams in the validation phase, which received a total of 1750 submissions. The testing phase garnered submissions from 28 of those teams, which represents 28 unique prediction methods. On average, over the course of the validation phase, participants improved the dose and DVH scores of their models by a factor of 2.7 and 5.7, respectively. In the testing phase one model achieved the best dose score (2.429) and DVH score (1.478), which were both significantly better than the dose score (2.564) and the DVH score (1.529) that was achieved by the runner-up models. Lastly, many of the top performing teams reported that they used generalizable techniques (e.g., ensembles) to achieve higher performance than their competition. CONCLUSION: OpenKBP is the first competition for knowledge-based planning research. The Challenge helped launch the first platform that enables researchers to compare KBP prediction methods fairly and consistently using a large open-source dataset and standardized metrics. OpenKBP has also democratized KBP research by making it accessible to everyone, which should help accelerate the progress of KBP research. The OpenKBP datasets are available publicly to help benchmark future KBP research.

Analysis of Classification Methods for Diagnosis of Pulmonary Nodules in CT Images

  • Baboo, Capt Dr S Santhosh
  • Iyyapparaj, E
IOSR Journal of Electrical and Electronics Engineering 2017 Journal Article, cited 0 times
Website
The main aim of this work is to propose a novel Computer-aided detection (CAD) system based on a Contextual clustering combined with region growing for assisting radiologists in early identification of lung cancer from computed tomography(CT) scans. Instead of using conventional thresholding approach, this proposed work uses Contextual Clustering which yields a more accurate segmentation of the lungs from the chest volume. Following segmentation GLCM features are extracted which are then classified using three different classifiers namely Random forest, SVM and k-NN.

Detection of Brain Tumour in MRI Scan Images using Tetrolet Transform and SVM Classifier

  • Babu, B Shoban
  • Varadarajan, S
Indian Journal of Science and Technology 2017 Journal Article, cited 1 times
Website

BIOMEDICAL IMAGE RETRIEVAL USING LBWP

  • Babu, Joyce Sarah
  • Mathew, Soumya
  • Simon, Rini
International Research Journal of Engineering and Technology 2017 Journal Article, cited 0 times
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Optimized convolutional neural network by firefly algorithm for magnetic resonance image classification of glioma brain tumor grade

  • Bacanin, Nebojsa
  • Bezdan, Timea
  • Venkatachalam, K.
  • Al-Turjman, Fadi
Journal of Real-Time Image Processing 2021 Journal Article, cited 0 times
Website
The most frequent brain tumor types are gliomas. The magnetic resonance imaging technique helps to make the diagnosis of brain tumors. It is hard to get the diagnosis in the early stages of the glioma brain tumor, although the specialist has a lot of experience. Therefore, for the magnetic resonance imaging interpretation, a reliable and efficient system is required which helps the doctor to make the diagnosis in early stages. To make classification of the images, to which class the glioma belongs, convolutional neural networks, which proved that they can obtain an excellent performance in the image classification tasks, can be used. Convolutional network hyperparameters’ tuning is a very important issue in this domain for achieving high accuracy on the image classification; however, this task takes a lot of computational time. Approaching this issue, in this manuscript, we propose a metaheuristics method to automatically find the near-optimal values of convolutional neural network hyperparameters based on a modified firefly algorithm and develop a system for automatic image classification of glioma brain tumor grades from magnetic resonance imaging. First, we have tested the proposed modified algorithm on the set of standard unconstrained benchmark functions and the performance is compared to the original algorithm and other modified variants. Upon verifying the efficiency of the proposed approach in general, it is applied for hyperparameters’ optimization of the convolutional neural network. The IXI dataset and the cancer imaging archive with more collections of data are used for evaluation purposes, and additionally, the method is evaluated on the axial brain tumor images. The obtained experimental results and comparative analysis with other state-of-the-art algorithms tested under the same conditions show the robustness and efficiency of the proposed method.

Virtual clinical trial for task-based evaluation of a deep learning synthetic mammography algorithm

  • Badal, Andreu
  • Cha, Kenny H.
  • Divel, Sarah E.
  • Graff, Christian G.
  • Zeng, Rongping
  • Badano, Aldo
2019 Conference Proceedings, cited 0 times
Website
Image processing algorithms based on deep learning techniques are being developed for a wide range of medical applications. Processed medical images are typically evaluated with the same kind of image similarity metrics used for natural scenes, disregarding the medical task for which the images are intended. We propose a com- putational framework to estimate the clinical performance of image processing algorithms using virtual clinical trials. The proposed framework may provide an alternative method for regulatory evaluation of non-linear image processing algorithms. To illustrate this application of virtual clinical trials, we evaluated three algorithms to compute synthetic mammograms from digital breast tomosynthesis (DBT) scans based on convolutional neural networks previously used for denoising low dose computed tomography scans. The inputs to the networks were one or more noisy DBT projections, and the networks were trained to minimize the difference between the output and the corresponding high dose mammogram. DBT and mammography images simulated with the Monte Carlo code MC-GPU using realistic breast phantoms were used for network training and validation. The denoising algorithms were tested in a virtual clinical trial by generating 3000 synthetic mammograms from the public VICTRE dataset of simulated DBT scans. The detectability of a calcification cluster and a spiculated mass present in the images was calculated using an ensemble of 30 computational channelized Hotelling observers. The signal detectability results, which took into account anatomic and image reader variability, showed that the visibility of the mass was not affected by the post-processing algorithm, but that the resulting slight blurring of the images severely impacted the visibility of the calcification cluster. The evaluation of the algorithms using the pixel-based metrics peak signal to noise ratio and structural similarity in image patches was not able to predict the reduction in performance in the detectability of calcifications. These two metrics are computed over the whole image and do not consider any particular task, and might not be adequate to estimate the diagnostic performance of the post-processed images.

Mammography and breast tomosynthesis simulator for virtual clinical trials

  • Badal, Andreu
  • Sharma, Diksha
  • Graff, Christian G.
  • Zeng, Rongping
  • Badano, Aldo
Computer Physics Communications 2021 Journal Article, cited 0 times
Website
Computer modeling and simulations are increasingly being used to predict the clinical performance of x-ray imaging devices in silico, and to generate synthetic patient images for training and testing of machine learning algorithms. We present a detailed description of the computational models implemented in the open source GPU-accelerated Monte Carlo x-ray imaging simulation code MC-GPU. This code, originally developed to simulate radiography and computed tomography, has been extended to replicate a commercial full-field digital mammography and digital breast tomosynthesis (DBT) device. The code was recently used to image 3000 virtual breast models with the aim of reproducing in silico a clinical trial used in support of the regulatory approval of DBT as a replacement of mammography for breast cancer screening. The updated code implements a more realistic x-ray source model (extended 3D focal spot, tomosynthesis acquisition trajectory, tube motion blurring) and an improved detector model (direct-conversion Selenium detector with depth-of-interaction effects, fluorescence tracking, electronic noise and anti-scatter grid). The software uses a high resolution voxelized geometry model to represent the breast anatomy. To reduce the GPU memory requirements, the code stores the voxels in memory within a binary tree structure. The binary tree is an efficient compression mechanism because many voxels with the same composition are combined in common tree branches while preserving random access to the phantom composition at any location. A delta scattering ray-tracing algorithm which does not require computing ray-voxel interfaces is used to minimize memory access. Multiple software verification and validation steps intended to establish the credibility of the implemented computational models are reported. The software verification was done using a digital quality control phantom and an ideal pinhole camera. The validation was performed reproducing standard bench testing experiments used in clinical practice and comparing with experimental measurements. A sensitivity study intended to assess the robustness of the simulated results to variations in some of the input parameters was performed using an in silico clinical trial pipeline with simulated lesions and mathematical observers. We show that MC-GPU is able to simulate x-ray projections that incorporate many of the sources of variability found in clinical images, and that the simulated results are robust to some uncertainty in the input parameters. Limitations of the implemented computational models are discussed. Program summary Program title: MCGPU_VICTRE CPC Library link to program files: http://dx.doi.org/10.17632/k5x2bsf27m.1 Licensing provisions: CC0 1.0 Programming language: C (with NVIDIA CUDA extensions) Nature of problem: The health risks associated with ionizing radiation impose a limit to the amount of clinical testing that can be done with x-ray imaging devices. In addition, radiation dose cannot be directly measured inside the body. For these reasons, a computational replica of an x-ray imaging device that simulates radiographic images of synthetic anatomical phantoms is of great value for device evaluation. The simulated radiographs and dosimetric estimates can be used for system design and optimization, task-based evaluation of image quality, machine learning software training, and in silico imaging trials. Solution method: Computational models of a mammography x-ray source and detector have been implemented. X-ray transport through matter is simulated using Monte Carlo methods customized for parallel execution in multiple Graphics Processing Units. The input patient anatomy is represented by voxels, which are efficiently stored in the video memory using a new binary tree structure compression mechanism.

Survival time prediction by integrating cox proportional hazards network and distribution function network

  • Baek, Eu-Tteum
  • Yang, Hyung Jeong
  • Kim, Soo Hyung
  • Lee, Guee Sang
  • Oh, In-Jae
  • Kang, Sae-Ryung
  • Min, Jung-Joon
BMC Bioinformatics 2021 Journal Article, cited 0 times
Website
BACKGROUND: The Cox proportional hazards model is commonly used to predict hazard ratio, which is the risk or probability of occurrence of an event of interest. However, the Cox proportional hazard model cannot directly generate an individual survival time. To do this, the survival analysis in the Cox model converts the hazard ratio to survival times through distributions such as the exponential, Weibull, Gompertz or log-normal distributions. In other words, to generate the survival time, the Cox model has to select a specific distribution over time. RESULTS: This study presents a method to predict the survival time by integrating hazard network and a distribution function network. The Cox proportional hazards network is adapted in DeepSurv for the prediction of the hazard ratio and a distribution function network applied to generate the survival time. To evaluate the performance of the proposed method, a new evaluation metric that calculates the intersection over union between the predicted curve and ground truth was proposed. To further understand significant prognostic factors, we use the 1D gradient-weighted class activation mapping method to highlight the network activations as a heat map visualization over an input data. The performance of the proposed method was experimentally verified and the results compared to other existing methods. CONCLUSIONS: Our results confirmed that the combination of the two networks, Cox proportional hazards network and distribution function network, can effectively generate accurate survival time.

Technical and Clinical Factors Affecting Success Rate of a Deep Learning Method for Pancreas Segmentation on CT

  • Bagheri, Mohammad Hadi
  • Roth, Holger
  • Kovacs, William
  • Yao, Jianhua
  • Farhadi, Faraz
  • Li, Xiaobai
  • Summers, Ronald M
Acad Radiol 2019 Journal Article, cited 0 times
Website
PURPOSE: Accurate pancreas segmentation has application in surgical planning, assessment of diabetes, and detection and analysis of pancreatic tumors. Factors that affect pancreas segmentation accuracy have not been previously reported. The purpose of this study is to identify technical and clinical factors that adversely affect the accuracy of pancreas segmentation on CT. METHOD AND MATERIALS: In this IRB and HIPAA compliant study, a deep convolutional neural network was used for pancreas segmentation in a publicly available archive of 82 portal-venous phase abdominal CT scans of 53 men and 29 women. The accuracies of the segmentations were evaluated by the Dice similarity coefficient (DSC). The DSC was then correlated with demographic and clinical data (age, gender, height, weight, body mass index), CT technical factors (image pixel size, slice thickness, presence or absence of oral contrast), and CT imaging findings (volume and attenuation of pancreas, visceral abdominal fat, and CT attenuation of the structures within a 5 mm neighborhood of the pancreas). RESULTS: The average DSC was 78% +/- 8%. Factors that were statistically significantly correlated with DSC included body mass index (r=0.34, p < 0.01), visceral abdominal fat (r=0.51, p < 0.0001), volume of the pancreas (r=0.41, p=0.001), standard deviation of CT attenuation within the pancreas (r=0.30, p=0.01), and median and average CT attenuation in the immediate neighborhood of the pancreas (r = -0.53, p < 0.0001 and r=-0.52, p < 0.0001). There were no significant correlations between the DSC and the height, gender, or mean CT attenuation of the pancreas. CONCLUSION: Increased visceral abdominal fat and accumulation of fat within or around the pancreas are major factors associated with more accurate segmentation of the pancreas. Potential applications of our findings include assessment of pancreas segmentation difficulty of a particular scan or dataset and identification of methods that work better for more challenging pancreas segmentations.

Imaging genomics in cancer research: limitations and promises

  • Bai, Harrison X
  • Lee, Ashley M
  • Yang, Li
  • Zhang, Paul
  • Davatzikos, Christos
  • Maris, John M
  • Diskin, Sharon J
The British journal of radiology 2016 Journal Article, cited 28 times
Website

BraTS Multimodal Brain Tumor Segmentation Challenge

  • Bakas, Spyridon
2017 Conference Proceedings, cited 2030 times
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Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features

  • Bakas, Spyridon
  • Akbari, Hamed
  • Sotiras, Aristeidis
  • Bilello, Michel
  • Rozycki, Martin
  • Kirby, Justin S.
  • Freymann, John B.
  • Farahani, Keyvan
  • Davatzikos, Christos
Scientific data 2017 Journal Article, cited 1036 times
Website
Gliomas belong to a group of central nervous system tumors, and consist of various sub-regions. Gold standard labeling of these sub-regions in radiographic imaging is essential for both clinical and computational studies, including radiomic and radiogenomic analyses. Towards this end, we release segmentation labels and radiomic features for all pre-operative multimodal magnetic resonance imaging (MRI) (n=243) of the multi-institutional glioma collections of The Cancer Genome Atlas (TCGA), publicly available in The Cancer Imaging Archive (TCIA). Pre-operative scans were identified in both glioblastoma (TCGA-GBM, n=135) and low-grade-glioma (TCGA-LGG, n=108) collections via radiological assessment. The glioma sub-region labels were produced by an automated state-of-the-art method and manually revised by an expert board-certified neuroradiologist. An extensive panel of radiomic features was extracted based on the manually-revised labels. This set of labels and features should enable i) direct utilization of the TCGA/TCIA glioma collections towards repeatable, reproducible and comparative quantitative studies leading to new predictive, prognostic, and diagnostic assessments, as well as ii) performance evaluation of computer-aided segmentation methods, and comparison to our state-of-the-art method.

GLISTRboost: Combining Multimodal MRI Segmentation, Registration, and Biophysical Tumor Growth Modeling with Gradient Boosting Machines for Glioma Segmentation.

  • Bakas, S.
  • Zeng, K.
  • Sotiras, A.
  • Rathore, S.
  • Akbari, H.
  • Gaonkar, B.
  • Rozycki, M.
  • Pati, S.
  • Davatzikos, C.
Brainlesion 2016 Journal Article, cited 49 times
Website
We present an approach for segmenting low- and high-grade gliomas in multimodal magnetic resonance imaging volumes. The proposed approach is based on a hybrid generative-discriminative model. Firstly, a generative approach based on an Expectation-Maximization framework that incorporates a glioma growth model is used to segment the brain scans into tumor, as well as healthy tissue labels. Secondly, a gradient boosting multi-class classification scheme is used to refine tumor labels based on information from multiple patients. Lastly, a probabilistic Bayesian strategy is employed to further refine and finalize the tumor segmentation based on patient-specific intensity statistics from the multiple modalities. We evaluated our approach in 186 cases during the training phase of the BRAin Tumor Segmentation (BRATS) 2015 challenge and report promising results. During the testing phase, the algorithm was additionally evaluated in 53 unseen cases, achieving the best performance among the competing methods.

Predicting Lung Cancer Survival Time Using Deep Learning Techniques

  • Baker, Qanita Bani
  • Gharaibeh, Maram
  • Al-Harahsheh, Yara
2021 Conference Paper, cited 0 times
Website
Lung cancer is one of the most commonly diagnosed cancer. Most studies found that lung cancer patients have a survival time up to 5 years after the cancer is found. An accurate prognosis is the most critical aspect of a clinical decision-making process for patients. predicting patients' survival time helps healthcare professionals to make treatment recommendations based on the prediction. In this paper, we used various deep learning methods to predict the survival time of Non-Small Cell Lung Cancer (NSCLC) patients in days which has been evaluated on clinical and radiomics dataset. The dataset was extracted from computerized tomography (CT) images that contain data for 300 patients. The concordance index (C-index) was used to evaluate the models. We applied several deep learning approaches and the best accuracy gained is 70.05% on the OWKIN task using Multilayer Perceptron (MLP) which outperforms the baseline model provided by the OWKIN task organizers

A radiogenomic dataset of non-small cell lung cancer

  • Bakr, Shaimaa
  • Gevaert, Olivier
  • Echegaray, Sebastian
  • Ayers, Kelsey
  • Zhou, Mu
  • Shafiq, Majid
  • Zheng, Hong
  • Benson, Jalen Anthony
  • Zhang, Weiruo
  • Leung, Ann NC
Scientific data 2018 Journal Article, cited 1 times
Website

Secure telemedicine using RONI halftoned visual cryptography without pixel expansion

  • Bakshi, Arvind
  • Patel, Anoop Kumar
Journal of Information Security and ApplicationsJ Inf Secur Appl 2019 Journal Article, cited 0 times
Website
To provide quality healthcare services worldwide telemedicine is a well-known technique. It delivers healthcare services remotely. For the diagnosis of disease and prescription by the doctor, lots of information is needed to be shared over public and private channels. Medical information like MRI, X-Ray, CT-scan etc. contains very personal information and needs to be secured. Security like confidentiality, privacy, and integrity of medical data is still a challenge. It is observed that the existing security techniques like digital watermarking, encryption are not efficient for real-time use. This paper investigates the problem and provides the solution of security considering major aspects, using Visual Cryptography (VC). The proposed algorithm creates shares for parts of the image which does not have relevant information. All the information which contains data related to the disease is supposed to be relevant and is marked as the region of interest (ROI). The integrity of the image is maintained by inserting some information in the region of non-interest (RONI). All the shares generated are transmitted over different channels and embedded information is decrypted by overlapping (in XOR fashion) shares in theta(1) time. Visual perception of all the results discussed in this article is very clear. The proposed algorithm has performance metrics as PSNR (peak signal-to-noise ratio), SSIM (structure similarity matrix), and Accuracy having values 22.9452, 0.9701, and 99.8740 respectively. (C) 2019 Elsevier Ltd. All rights reserved.

Test–Retest Reproducibility Analysis of Lung CT Image Features

  • Balagurunathan, Yoganand
  • Kumar, Virendra
  • Gu, Yuhua
  • Kim, Jongphil
  • Wang, Hua
  • Liu, Ying
  • Goldgof, Dmitry B
  • Hall, Lawrence O
  • Korn, Rene
  • Zhao, Binsheng
2014 Journal Article, cited 85 times
Website
Quantitative size, shape, and texture features derived from computed tomographic (CT) images may be useful as predictive, prognostic, or response biomarkers in non-small cell lung cancer (NSCLC). However, to be useful, such features must be reproducible, non-redundant, and have a large dynamic range. We developed a set of quantitative three-dimensional (3D) features to describe segmented tumors and evaluated their reproducibility to select features with high potential to have prognostic utility. Thirty-two patients with NSCLC were subjected to unenhanced thoracic CT scans acquired within 15 min of each other under an approved protocol. Primary lung cancer lesions were segmented using semi-automatic 3D region growing algorithms. Following segmentation, 219 quantitative 3D features were extracted from each lesion, corresponding to size, shape, and texture, including features in transformed spaces (laws, wavelets). The most informative features were selected using the concordance correlation coefficient across test–retest, the biological range and a feature independence measure. There were 66 (30.14 %) features with concordance correlation coefficient ≥ 0.90 across test–retest and acceptable dynamic range. Of these, 42 features were non-redundant after grouping features with R2Bet ≥ 0.95. These reproducible features were found to be predictive of radiological prognosis. The area under the curve (AUC) was 91 % for a size-based feature and 92 % for the texture features (runlength, laws). We tested the ability of image features to predict a radiological prognostic score on an independent NSCLC (39 adenocarcinoma) samples, the AUC for texture features (runlength emphasis, energy) was 0.84 while the conventional size-based features (volume, longest diameter) was 0.80. Test–retest and correlation analyses have identified non-redundant CT image features with both high intra-patient reproducibility and inter-patient biological range. Thus making the case that quantitative image features are informative and prognostic biomarkers for NSCLC.

Quantitative Imaging features Improve Discrimination of Malignancy in Pulmonary nodules

  • Balagurunathan, Yoganand
  • Schabath, Matthew B.
  • Wang, Hua
  • Liu, Ying
  • Gillies, Robert J.
2019 Journal Article, cited 0 times
Website
Pulmonary nodules are frequently detected radiological abnormalities in lung cancer screening. Nodules of the highest- and lowest-risk for cancer are often easily diagnosed by a trained radiologist there is still a high rate of indeterminate pulmonary nodules (IPN) of unknown risk. Here, we test the hypothesis that computer extracted quantitative features ("radiomics") can provide improved risk-assessment in the diagnostic setting. Nodules were segmented in 3D and 219 quantitative features are extracted from these volumes. Using these features novel malignancy risk predictors are formed with various stratifications based on size, shape and texture feature categories. We used images and data from the National Lung Screening Trial (NLST), curated a subset of 479 participants (244 for training and 235 for testing) that included incident lung cancers and nodule-positive controls. After removing redundant and non-reproducible features, optimal linear classifiers with area under the receiver operator characteristics (AUROC) curves were used with an exhaustive search approach to find a discriminant set of image features, which were validated in an independent test dataset. We identified several strong predictive models, using size and shape features the highest AUROC was 0.80. Using non-size based features the highest AUROC was 0.85. Combining features from all the categories, the highest AUROC were 0.83.

Bone-Cancer Assessment and Destruction Pattern Analysis in Long-Bone X-ray Image

  • Bandyopadhyay, Oishila
  • Biswas, Arindam
  • Bhattacharya, Bhargab B
J Digit Imaging 2018 Journal Article, cited 0 times
Website
Bone cancer originates from bone and rapidly spreads to the rest of the body affecting the patient. A quick and preliminary diagnosis of bone cancer begins with the analysis of bone X-ray or MRI image. Compared to MRI, an X-ray image provides a low-cost diagnostic tool for diagnosis and visualization of bone cancer. In this paper, a novel technique for the assessment of cancer stage and grade in long bones based on X-ray image analysis has been proposed. Cancer-affected bone images usually appear with a variation in bone texture in the affected region. A fusion of different methodologies is used for the purpose of our analysis. In the proposed approach, we extract certain features from bone X-ray images and use support vector machine (SVM) to discriminate healthy and cancerous bones. A technique based on digital geometry is deployed for localizing cancer-affected regions. Characterization of the present stage and grade of the disease and identification of the underlying bone-destruction pattern are performed using a decision tree classifier. Furthermore, the method leads to the development of a computer-aided diagnostic tool that can readily be used by paramedics and doctors. Experimental results on a number of test cases reveal satisfactory diagnostic inferences when compared with ground truth known from clinical findings.

Glioma Classification Using Deep Radiomics

  • Banerjee, Subhashis
  • Mitra, Sushmita
  • Masulli, Francesco
  • Rovetta, Stefano
SN Computer Science 2020 Journal Article, cited 1 times
Website
Glioma constitutes $$80\%$$80%of malignant primary brain tumors in adults, and is usually classified as high-grade glioma (HGG) and low-grade glioma (LGG). The LGG tumors are less aggressive, with slower growth rate as compared to HGG, and are responsive to therapy. Tumor biopsy being challenging for brain tumor patients, noninvasive imaging techniques like magnetic resonance imaging (MRI) have been extensively employed in diagnosing brain tumors. Therefore, development of automated systems for the detection and prediction of the grade of tumors based on MRI data becomes necessary for assisting doctors in the framework of augmented intelligence. In this paper, we thoroughly investigate the power of deep convolutional neural networks (ConvNets) for classification of brain tumors using multi-sequence MR images. We propose novel ConvNet models, which are trained from scratch, on MRI patches, slices, and multi-planar volumetric slices. The suitability of transfer learning for the task is next studied by applying two existing ConvNets models (VGGNet and ResNet) trained on ImageNet dataset, through fine-tuning of the last few layers. Leave-one-patient-out testing, and testing on the holdout dataset are used to evaluate the performance of the ConvNets. The results demonstrate that the proposed ConvNets achieve better accuracy in all cases where the model is trained on the multi-planar volumetric dataset. Unlike conventional models, it obtains a testing accuracy of $$95\%$$95%for the low/high grade glioma classification problem. A score of $$97\%$$97%is generated for classification of LGG with/without 1p/19q codeletion, without any additional effort toward extraction and selection of features. We study the properties of self-learned kernels/ filters in different layers, through visualization of the intermediate layer outputs. We also compare the results with that of state-of-the-art methods, demonstrating a maximum improvement of $$7\%$$7%on the grading performance of ConvNets and $$9\%$$9%on the prediction of 1p/19q codeletion status.

A novel fully automated MRI-based deep-learning method for classification of IDH mutation status in brain gliomas

  • Bangalore Yogananda, Chandan Ganesh
  • Shah, Bhavya R
  • Vejdani-Jahromi, Maryam
  • Nalawade, Sahil S
  • Murugesan, Gowtham K
  • Yu, Frank F
  • Pinho, Marco C
  • Wagner, Benjamin C
  • Mickey, Bruce
  • Patel, Toral R
2020 Journal Article, cited 4 times
Website

A New Adaptive-Weighted Fusion Rule for Wavelet based PET/CT Fusion

  • Barani, R
  • Sumathi, M
International Journal of Signal Processing, Image Processing and Pattern Recognition 2016 Journal Article, cited 1 times
Website
In recent years the Wavelet Transform (WT) had an important role in various applications of signal and image processing. In Image Processing, WT is more useful in many domains like image denoising, feature segmentation, compression, restoration, image fusion, etc. In WT based image fusion, initially the source images are decomposed into approximation and detail coefficients and followed by combining the coefficients using the suitable fusion rules. The resultant fused image is reconstructed by applying inverse WT on the combined coefficients. This paper proposes a new adaptive fusion rule for combining the approximation coefficients of CT and PET images. The Excellency of the proposed fusion rule is stamped by measuring the image information metrics, EOG, SD and ENT on the decomposed approximation coefficients. On the other hand, the detail coefficients are combined using several existing fusion rules. The resultant fused images are quantitatively analyzed using the non-reference image quality, image fusion and error metrics. The analysis declares that the newly proposed fusion rule is more suitable for extracting the complementary information from CT and PET images and also produces the fused image which is rich in content with good contrast and sharpness.

Interreader Variability of Dynamic Contrast-enhanced MRI of Recurrent Glioblastoma: The Multicenter ACRIN 6677/RTOG 0625 Study

  • Barboriak, Daniel P
  • Zhang, Zheng
  • Desai, Pratikkumar
  • Snyder, Bradley S
  • Safriel, Yair
  • McKinstry, Robert C
  • Bokstein, Felix
  • Sorensen, Gregory
  • Gilbert, Mark R
  • Boxerman, Jerrold L
RadiologyRadiology 2019 Journal Article, cited 2 times
Website
Purpose To evaluate factors contributing to interreader variation (IRV) in parameters measured at dynamic contrast material-enhanced (DCE) MRI in patients with glioblastoma who were participating in a multicenter trial. Materials and Methods A total of 18 patients (mean age, 57 years +/- 13 [standard deviation]; 10 men) who volunteered for the advanced imaging arm of ACRIN 6677, a substudy of the RTOG 0625 clinical trial for recurrent glioblastoma treatment, underwent analyzable DCE MRI at one of four centers. The 78 imaging studies were analyzed centrally to derive the volume transfer constant (K(trans)) for gadolinium between blood plasma and tissue extravascular extracellular space, fractional volume of the extracellular extravascular space (ve), and initial area under the gadolinium concentration curve (IAUGC). Two independently trained teams consisting of a neuroradiologist and a technologist segmented the enhancing tumor on three-dimensional spoiled gradient-recalled acquisition in the steady-state images. Mean and median parameter values in the enhancing tumor were extracted after registering segmentations to parameter maps. The effect of imaging time relative to treatment, map quality, imager magnet and sequence, average tumor volume, and reader variability in tumor volume on IRV was studied by using intraclass correlation coefficients (ICCs) and linear mixed models. Results Mean interreader variations (+/- standard deviation) (difference as a percentage of the mean) for mean and median IAUGC, mean and median K(trans), and median ve were 18% +/- 24, 17% +/- 23, 27% +/- 34, 16% +/- 27, and 27% +/- 34, respectively. ICCs for these metrics ranged from 0.90 to 1.0 for baseline and from 0.48 to 0.76 for posttreatment examinations. Variability in reader-derived tumor volume was significantly related to IRV for all parameters. Conclusion Differences in reader tumor segmentations are a significant source of interreader variation for all dynamic contrast-enhanced MRI parameters. (c) RSNA, 2018 Online supplemental material is available for this article. See also the editorial by Wolf in this issue.

Variational Quantum Denoising Technique for Medical Images

  • Barbu, Tudor
2020 Conference Paper, cited 2 times
Website
A novel variational restoration framework for the medical images corrupted by quantum, or Poisson, noise is proposed in this research paper. The considered approach is using a variational scheme that leads to a nonlinear fourth-order PDE-based model. That partial differential equation model is then solved numerically by developing a consistent finite difference-based numerical approximation scheme converging to its variational solution. The obtained numerical algorithm removes successfully the quantum noise from the medical images, preserves their details, and outperforms other shot noise filtering solutions.

Pathologically-Validated Tumor Prediction Maps in MRI

  • Barrington, Alex
2019 Thesis, cited 0 times
Website
Glioblastoma (GBM) is an aggressive cancer with an average 5-year survival rate of about 5%. Following treatment with surgery, radiation, and chemotherapy, diagnosing tumor recurrence requires serial magnetic resonance imaging (MRI) scans. Infiltrative tumor cells beyond gadolinium enhancement on T1-weighted MRI are difficult to detect. This study therefore aims to improve tumor detection beyond traditional tumor margins. To accomplish this, a neural network model was trained to classify tissue samples as ‘tumor’ or ‘not tumor’. This model was then used to classify thousands of tiles from histology samples acquired at autopsy with known MRI locations on the patient’s final clinical MRI scan. This combined radiological-pathological (rad-path) dataset was then treated as a ground truth to train a second model for predicting tumor presence from MRI alone. Predictive maps were created for seven patients left out of the training steps, and tissue samples were tested to determine the model’s accuracy. The final model produced a receiver operator characteristic (ROC) area under the curve (AUC) of 0.70. This study demonstrates a new method for detecting infiltrative tumor beyond conventional radiologist defined margins based on neural networks applied to rad-path datasets in glioblastoma.

Equating quantitative emphysema measurements on different CT image reconstructions

  • Bartel, Seth T
  • Bierhals, Andrew J
  • Pilgram, Thomas K
  • Hong, Cheng
  • Schechtman, Kenneth B
  • Conradi, Susan H
  • Gierada, David S
Medical Physics 2011 Journal Article, cited 15 times
Website
PURPOSE: To mathematically model the relationship between CT measurements of emphysema obtained from images reconstructed using different section thicknesses and kernels and to evaluate the accuracy of the models for converting measurements to those of a reference reconstruction. METHODS: CT raw data from the lung cancer screening examinations of 138 heavy smokers were reconstructed at 15 different combinations of section thickness and kernel. An emphysema index was quantified as the percentage of the lung with attenuation below -950 HU (EI950). Linear, quadratic, and power functions were used to model the relationship between EI950 values obtained with a reference 1 mm, medium smooth kernel reconstruction and values from each of the other 14 reconstructions. Preferred models were selected using the corrected Akaike information criterion (AICc), coefficients of determination (R2), and residuals (conversion errors), and cross-validated by a jackknife approach using the leave-one-out method. RESULTS: The preferred models were power functions, with model R2 values ranging from 0.949 to 0.998. The errors in converting EI950 measurements from other reconstructions to the 1 mm, medium smooth kernel reconstruction in leave-one-out testing were less than 3.0 index percentage points for all reconstructions, and less than 1.0 index percentage point for five reconstructions. Conversion errors were related in part to image noise, emphysema distribution, and attenuation histogram parameters. Conversion inaccuracy related to increased kernel sharpness tended to be reduced by increased section thickness. CONCLUSIONS: Image reconstruction-related differences in quantitative emphysema measurements were successfully modeled using power functions.

A Heterogeneous and Multi-Range Soft-Tissue Deformation Model for Applications in Adaptive Radiotherapy

  • Bartelheimer, Kathrin
2020 Thesis, cited 0 times
Website
Abstract During fractionated radiotherapy, anatomical changes result in uncertainties in the applied dose distribution. With increasing steepness of applied dose gradients, the relevance of patient deformations increases. Especially in proton therapy, small anatomical changes in the order of millimeters can result in large range uncertainties and therefore in substantial deviations from the planned dose. To quantify the anatomical changes, deformation models are required. With upcoming MR-guidance, the soft-tissue deformations gain visibility, but so far only few soft-tissue models meeting the requirements of high-precision radiotherapy exist. Most state-of-the-art models either lack anatomical detail or exhibit long computation times. In this work, a fast soft-tissue deformation model is developed which is capable of considering tissue properties of heterogeneous tissue. The model is based on the chainmail (CM)-concept, which is improved by three basic features. For the first time, rotational degrees of freedom are introduced into the CM-concept to improve the characteristic deformation behavior. A novel concept for handling multiple deformation initiators is developed to cope with global deformation input. And finally, a concept for handling various shapes of deformation input is proposed to provide a high flexibility concerning the design of deformation input. To demonstrate the model flexibility, it was coupled to a kinematic skeleton model for the head and neck region, which provides anatomically correct deformation input for the bones. For exemplary patient CTs, the combined model was shown to be capable of generating artificially deformed CT images with realistic appearance. This was achieved for small-range deformations in the order of interfractional deformations, as well as for large-range deformations like an arms-up to arms-down deformation, as can occur between images of different modalities. The deformation results showed a strong improvement in biofidelity, compared to the original chainmail-concept, as well as compared to clinically used image-based deformation methods. The computation times for the model are in the order of 30 min for single-threaded calculations, by simple code parallelization times in the order of 1 min can be achieved. Applications that require realistic forward deformations of CT images will benefit from the improved biofidelity of the developed model. Envisioned applications are the generation of plan libraries and virtual phantoms, as well as data augmentation for deep learning approaches. Due to the low computation times, the model is also well suited for image registration applications. In this context, it will contribute to an improved calculation of accumulated dose, as is required in high-precision adaptive radiotherapy. Translation of abstract (German) Anatomische Veränderungen im Laufe der fraktionierten Strahlentherapie erzeugen Unsicherheiten in der tatsächlich applizierten Dosisverteilung. Je steiler die Dosisgradienten in der Verteilung sind, desto größer wird der Einfluss von Patientendeformationen. Insbesondere in der Protonentherapie erzeugen schon kleine anatomische Veränderungen im mm-Bereich große Unsicherheiten in der Reichweite und somit extreme Unterschiede zur geplanten Dosis. Um solche anatomischen Veränderungen zu quantifizieren, werden Deformationsmodelle benötigt. Durch die aufkommenden Möglichkeiten von MR-guidance gewinnt das Weichgewebe an Sichtbarkeit. Allerdings gibt es bisher nur wenige Modelle für Weichgewebe, welche den Anforderungen von hochpräziser Strahlentherapie genügen. Die meisten Modelle berücksichtigen entweder nicht genügend anatomische Details oder benötigen lange Rechenzeiten. In dieser Arbeit wird ein schnelles Deformationsmodell für Weichgewebe entwickelt, welches es ermöglicht, Gewebeeigenschaften von heterogenem Gewebe zu berücksichtigen. Dieses Modell basiert auf dem Chainmail (CM)-Konzept, welches um drei grundlegende Eigenschaften erweitert wird. Rotationsfreiheitsgrade werden in das CM-Konzept eingebracht, um das charakteristische Deformationsverhalten zu verbessern. Es wird ein neues Konzept für multiple Deformationsinitiatoren entwickelt, um mit globalem Deformationsinput umgehen zu können. Und zuletzt wird ein Konzept zum Umgang mit verschiedenen Formen von Deformationsinput vorgestellt, welches eine hohe Flexibilität für die Kopplung zu anderen Modellen ermöglicht. Um diese Flexibilität des Modells zu zeigen, wurde es mit einem kinematischen Skelettmodell für die Kopf-Hals-Region gekoppelt, welches anatomisch korrekten Input für die Knochen liefert. Basierend auf exemplarischen Patientendatensätzen wurde gezeigt, dass das gekoppelte Modell realistisch aussehende, künstlich deformierte CTs erzeugen kann. Dies war sowohl für eine kleine Deformation im Bereich von interfraktionellen Bewegungen als auch für eine große Deformation, wie z.B. eine arms-up zu arms-down Bewegung, welche zwischen multimodalen Bildern auftreten kann, möglich. Die Ergebnisse zeigen eine starke Verbesserung der Biofidelity im Vergleich zum CM-Modell, und auch im Vergleich zu klinisch eingesetzten bildbasierten Deformationsmodellen. Die Rechenzeiten für das Modell liegen im Bereich von 30 min für single-threaded Berechnungen. Durch einfache Code-Parallelisierung können Zeiten im Bereich von 1 min erreicht werden. Anwendungen, die realistische CTs aus Vorwärtsdeformationen benötigen, werden von der verbesserten Biofidelity des entwickelten Modells profitieren. Mögliche Anwendungen sind die Erstellung von Plan-Bibliotheken und virtuellen Phantomen sowie Daten-Augmentation für deep-learning Ansätze. Aufgrund der geringen Rechenzeiten ist das Modell auch für Anwendungen in der Bildregistrierung gut geeignet. In diesem Kontext wird es zu einer verbesserten Berechnung der akkumulierten Dosis beitragen, welche für hochpräzise adaptive Strahlentherapie benötigt wird.

Removing Mixture Noise from Medical Images Using Block Matching Filtering and Low-Rank Matrix Completion

  • Barzigar, Nafise
  • Roozgard, Aminmohammad
  • Verma, Pramode K
  • Cheng, Samuel
2012 Conference Proceedings, cited 2 times
Website

Machine Intelligence for Advanced Medical Data Analysis: Manifold Learning Approach

  • Bashiri, Fereshteh Sadat
2019 Thesis, cited 0 times
Website
In the current work, linear and non-linear manifold learning techniques, specifically Principle Component Analysis (PCA) and Laplacian Eigenmaps, are studied in detail. Their applications in medical image and shape analysis are investigated. In the first contribution, a manifold learning-based multi-modal image registration technique is developed, which results in a unified intensity system through intensity transformation between the reference and sensed images. The transformation eliminates intensity variations in multi-modal medical scans and hence facilitates employing well-studied monomodal registration techniques. The method can be used for registering multi-modal images with full and partial data. Next, a manifold learning-based scale invariant global shape descriptor is introduced. The proposed descriptor benefits from the capability of Laplacian Eigenmap in dealing with high dimensional data by introducing an exponential weighting scheme. It eliminates the limitations tied to the well-known cotangent weighting scheme, namely dependency on triangular mesh representation and high intra-class quality of 3D models. In the end, a novel descriptive model for diagnostic classification of pulmonary nodules is presented. The descriptive model benefits from structural differences between benign and malignant nodules for automatic and accurate prediction of a candidate nodule. It extracts concise and discriminative features automatically from the 3D surface structure of a nodule using spectral features studied in the previous work combined with a point cloud-based deep learning network. Extensive experiments have been conducted and have shown that the proposed algorithms based on manifold learning outperform several state-of-the-art methods. Advanced computational techniques with a combination of manifold learning and deep networks can play a vital role in effective healthcare delivery by providing a framework for several fundamental tasks in image and shape processing, namely, registration, classification, and detection of features of interest.

A novel decentralized model for storing and sharing neuroimaging data using ethereum blockchain and the interplanetary file system

  • Batchu, Sai
  • Henry, Owen S.
  • Hakim, Abraham A.
International Journal of Information Technology 2021 Journal Article, cited 0 times
Website
Current methods to store and transfer medical neuroimaging data raise issues with security and transparency, and novel protocols are needed. Ethereum smart contracts present an encouraging new option. Ethereum is an open-source platform that allows users to construct smart contracts—self-executable packages of code that exist in the Ethereum state and allow transactions under programmed conditions. The present study developed a proof-of-concept smart contract that stores patient brain tumor data such as patient identifier, disease, grade, chemotherapy drugs, and Karnofsky score. The InterPlanetary file system was used to efficiently store the image files, and the corresponding content identifier hashes were stored within the smart contracts. Testing with a private, proof-of-authority network required only 889 MB of memory per insertion to insert 350 patient records, while retrieval required 910 MB. Inserting 350 patient records required 907 ms. The concept presented in this study exemplifies the use of smart contracts and off chain data storage for efficient retrieval/insertion of medical neuroimaging data.

Variability of manual segmentation of the prostate in axial T2-weighted MRI: A multi-reader study

  • Becker, A. S.
  • Chaitanya, K.
  • Schawkat, K.
  • Müehlematter, U. J.
  • Hotker, A. M.
  • Konukoglu, E.
  • Donati, O. F.
Eur J Radiol 2019 Journal Article, cited 3 times
Website
PURPOSE: To evaluate the interreader variability in prostate and seminal vesicle (SV) segmentation on T2w MRI. METHODS: Six readers segmented the peripheral zone (PZ), transitional zone (TZ) and SV slice-wise on axial T2w prostate MRI examinations of n=80 patients. Twenty different similarity scores, including dice score (DS), Hausdorff distance (HD) and volumetric similarity coefficient (VS), were computed with the VISCERAL EvaluateSegmentation software for all structures combined and separately for the whole gland (WG=PZ+TZ), TZ and SV. Differences between base, midgland and apex were evaluated with DS slice-wise. Descriptive statistics for similarity scores were computed. Wilcoxon testing to evaluate differences of DS, HD and VS was performed. RESULTS: Overall segmentation variability was good with a mean DS of 0.859 (+/-SD=0.0542), HD of 36.6 (+/-34.9 voxels) and VS of 0.926 (+/-0.065). The WG showed a DS, HD and VS of 0.738 (+/-0.144), 36.2 (+/-35.6 vx) and 0.853 (+/-0.143), respectively. The TZ showed generally lower variability with a DS of 0.738 (+/-0.144), HD of 24.8 (+/-16 vx) and VS of 0.908 (+/-0.126). The lowest variability was found for the SV with DS of 0.884 (+/-0.0407), HD of 17 (+/-10.9 vx) and VS of 0.936 (+/-0.0509). We found a markedly lower DS of the segmentations in the apex (0.85+/-0.12) compared to the base (0.87+/-0.10, p<0.01) and the midgland (0.89+/-0.10, p<0.001). CONCLUSIONS: We report baseline values for interreader variability of prostate and SV segmentation on T2w MRI. Variability was highest in the apex, lower in the base, and lowest in the midgland.

Integration of proteomics with CT-based qualitative and radiomic features in high-grade serous ovarian cancer patients: an exploratory analysis

  • Beer, Lucian
  • Sahin, Hilal
  • Bateman, Nicholas W
  • Blazic, Ivana
  • Vargas, Hebert Alberto
  • Veeraraghavan, Harini
  • Kirby, Justin
  • Fevrier-Sullivan, Brenda
  • Freymann, John B
  • Jaffe, C Carl
European Radiology 2020 Journal Article, cited 1 times
Website

Anatomical DCE-MRI phantoms generated from glioma patient data

  • Beers, Andrew
  • Chang, Ken
  • Brown, James
  • Zhu, Xia
  • Sengupta, Dipanjan
  • Willke, Theodore L
  • Gerstner, Elizabeth
  • Rosen, Bruce
  • Kalpathy-Cramer, Jayashree
2018 Conference Proceedings, cited 0 times
Website

Multi‐site quality and variability analysis of 3D FDG PET segmentations based on phantom and clinical image data

  • Beichel, Reinhard R
  • Smith, Brian J
  • Bauer, Christian
  • Ulrich, Ethan J
  • Ahmadvand, Payam
  • Budzevich, Mikalai M
  • Gillies, Robert J
  • Goldgof, Dmitry
  • Grkovski, Milan
  • Hamarneh, Ghassan
Medical Physics 2017 Journal Article, cited 7 times
Website
PURPOSE: Radiomics utilizes a large number of image-derived features for quantifying tumor characteristics that can in turn be correlated with response and prognosis. Unfortunately, extraction and analysis of such image-based features is subject to measurement variability and bias. The challenge for radiomics is particularly acute in Positron Emission Tomography (PET) where limited resolution, a high noise component related to the limited stochastic nature of the raw data, and the wide variety of reconstruction options confound quantitative feature metrics. Extracted feature quality is also affected by tumor segmentation methods used to define regions over which to calculate features, making it challenging to produce consistent radiomics analysis results across multiple institutions that use different segmentation algorithms in their PET image analysis. Understanding each element contributing to these inconsistencies in quantitative image feature and metric generation is paramount for ultimate utilization of these methods in multi-institutional trials and clinical oncology decision making. METHODS: To assess segmentation quality and consistency at the multi-institutional level, we conducted a study of seven institutional members of the National Cancer Institute Quantitative Imaging Network. For the study, members were asked to segment a common set of phantom PET scans acquired over a range of imaging conditions as well as a second set of head and neck cancer (HNC) PET scans. Segmentations were generated at each institution using their preferred approach. In addition, participants were asked to repeat segmentations with a time interval between initial and repeat segmentation. This procedure resulted in overall 806 phantom insert and 641 lesion segmentations. Subsequently, the volume was computed from the segmentations and compared to the corresponding reference volume by means of statistical analysis. RESULTS: On the two test sets (phantom and HNC PET scans), the performance of the seven segmentation approaches was as follows. On the phantom test set, the mean relative volume errors ranged from 29.9 to 87.8% of the ground truth reference volumes, and the repeat difference for each institution ranged between -36.4 to 39.9%. On the HNC test set, the mean relative volume error ranged between -50.5 to 701.5%, and the repeat difference for each institution ranged between -37.7 to 31.5%. In addition, performance measures per phantom insert/lesion size categories are given in the paper. On phantom data, regression analysis resulted in coefficient of variation (CV) components of 42.5% for scanners, 26.8% for institutional approaches, 21.1% for repeated segmentations, 14.3% for relative contrasts, 5.3% for count statistics (acquisition times), and 0.0% for repeated scans. Analysis showed that the CV components for approaches and repeated segmentations were significantly larger on the HNC test set with increases by 112.7% and 102.4%, respectively. CONCLUSION: Analysis results underline the importance of PET scanner reconstruction harmonization and imaging protocol standardization for quantification of lesion volumes. In addition, to enable a distributed multi-site analysis of FDG PET images, harmonization of analysis approaches and operator training in combination with highly automated segmentation methods seems to be advisable. Future work will focus on quantifying the impact of segmentation variation on radiomics system performance.

Radiogenomic-Based Survival Risk Stratification of Tumor Habitat on Gd-T1w MRI Is Associated with Biological Processes in Glioblastoma

  • Beig, Niha
  • Bera, Kaustav
  • Prasanna, Prateek
  • Antunes, Jacob
  • Correa, Ramon
  • Singh, Salendra
  • Saeed Bamashmos, Anas
  • Ismail, Marwa
  • Braman, Nathaniel
  • Verma, Ruchika
  • Hill, Virginia B
  • Statsevych, Volodymyr
  • Ahluwalia, Manmeet S
  • Varadan, Vinay
  • Madabhushi, Anant
  • Tiwari, Pallavi
Clin Cancer Res 2020 Journal Article, cited 0 times
Website
PURPOSE: To (i) create a survival risk score using radiomic features from the tumor habitat on routine MRI to predict progression-free survival (PFS) in glioblastoma and (ii) obtain a biological basis for these prognostic radiomic features, by studying their radiogenomic associations with molecular signaling pathways. EXPERIMENTAL DESIGN: Two hundred three patients with pretreatment Gd-T1w, T2w, T2w-FLAIR MRI were obtained from 3 cohorts: The Cancer Imaging Archive (TCIA; n = 130), Ivy GAP (n = 32), and Cleveland Clinic (n = 41). Gene-expression profiles of corresponding patients were obtained for TCIA cohort. For every study, following expert segmentation of tumor subcompartments (necrotic core, enhancing tumor, peritumoral edema), 936 3D radiomic features were extracted from each subcompartment across all MRI protocols. Using Cox regression model, radiomic risk score (RRS) was developed for every protocol to predict PFS on the training cohort (n = 130) and evaluated on the holdout cohort (n = 73). Further, Gene Ontology and single-sample gene set enrichment analysis were used to identify specific molecular signaling pathway networks associated with RRS features. RESULTS: Twenty-five radiomic features from the tumor habitat yielded the RRS. A combination of RRS with clinical (age and gender) and molecular features (MGMT and IDH status) resulted in a concordance index of 0.81 (P < 0.0001) on training and 0.84 (P = 0.03) on the test set. Radiogenomic analysis revealed associations of RRS features with signaling pathways for cell differentiation, cell adhesion, and angiogenesis, which contribute to chemoresistance in GBM. CONCLUSIONS: Our findings suggest that prognostic radiomic features from routine Gd-T1w MRI may also be significantly associated with key biological processes that affect response to chemotherapy in GBM.

Radiogenomic analysis of hypoxia pathway is predictive of overall survival in Glioblastoma

  • Beig, N.
  • Patel, J.
  • Prasanna, P.
  • Hill, V.
  • Gupta, A.
  • Correa, R.
  • Bera, K.
  • Singh, S.
  • Partovi, S.
  • Varadan, V.
  • Ahluwalia, M.
  • Madabhushi, A.
  • Tiwari, P.
Sci RepScientific reports 2018 Journal Article, cited 5 times
Website
Hypoxia, a characteristic trait of Glioblastoma (GBM), is known to cause resistance to chemo-radiation treatment and is linked with poor survival. There is hence an urgent need to non-invasively characterize tumor hypoxia to improve GBM management. We hypothesized that (a) radiomic texture descriptors can capture tumor heterogeneity manifested as a result of molecular variations in tumor hypoxia, on routine treatment naive MRI, and (b) these imaging based texture surrogate markers of hypoxia can discriminate GBM patients as short-term (STS), mid-term (MTS), and long-term survivors (LTS). 115 studies (33 STS, 41 MTS, 41 LTS) with gadolinium-enhanced T1-weighted MRI (Gd-T1w) and T2-weighted (T2w) and FLAIR MRI protocols and the corresponding RNA sequences were obtained. After expert segmentation of necrotic, enhancing, and edematous/nonenhancing tumor regions for every study, 30 radiomic texture descriptors were extracted from every region across every MRI protocol. Using the expression profile of 21 hypoxia-associated genes, a hypoxia enrichment score (HES) was obtained for the training cohort of 85 cases. Mutual information score was used to identify a subset of radiomic features that were most informative of HES within 3-fold cross-validation to categorize studies as STS, MTS, and LTS. When validated on an additional cohort of 30 studies (11 STS, 9 MTS, 10 LTS), our results revealed that the most discriminative features of HES were also able to distinguish STS from LTS (p = 0.003).

Radiogenomic analysis of hypoxia pathway reveals computerized MRI descriptors predictive of overall survival in Glioblastoma

  • Beig, Niha
  • Patel, Jay
  • Prasanna, Prateek
  • Partovi, Sasan
  • Varadhan, Vinay
  • Madabhushi, Anant
  • Tiwari, Pallavi
2017 Conference Proceedings, cited 3 times
Website

Longitudinal fan-beam computed tomography dataset for head-and-neck squamous cell carcinoma patients

  • Bejarano, Tatiana
  • De Ornelas-Couto, Mariluz
  • Mihaylov, Ivaylo B.
Medical Physics 2019 Journal Article, cited 0 times
Website
Purpose To describe in detail a dataset consisting of longitudinal fan-beam computed tomography (CT) imaging to visualize anatomical changes in head-and-neck squamous cell carcinoma (HNSCC) patients throughout radiotherapy (RT) treatment course. Acquisition and validation methods This dataset consists of CT images from 31 HNSCC patients who underwent volumetric modulated arc therapy (VMAT). Patients had three CT scans acquired throughout the duration of the radiation treatment course. Pretreatment planning CT scans with a median of 13 days before treatment (range: 2–27), mid-treatment CT at 22 days after start of treatment (range: 13–38), and post-treatment CT 65 days after start of treatment (range: 35–192). Patients received RT treatment to a total dose of 58–70 Gy, using daily 2.0–2.20 Gy, fractions for 30–35 fractions. The fan-beam CT images were acquired using a Siemens 16-slice CT scanner head protocol with 120 kV and current of 400 mAs. A helical scan with 1 rotation per second was used with a slice thickness of 2 mm and table increment of 1.2 mm. In addition to the imaging data, contours of anatomical structures for RT, demographic, and outcome measurements are provided. Data format and usage notes The dataset with DICOM files including images, RTSTRUCT files, and RTDOSE files can be found and publicly accessed in the Cancer Imaging Archive (TCIA, http://www.cancerimagingarchive.net/) as collection Head-and-neck squamous cell carcinoma patients with CT taken during pretreatment, mid-treatment, and post-treatment (HNSCC-3DCT-RT). Discussion This is the first dataset to date in TCIA which provides a collection of multiple CT imaging studies (pretreatment, mid-treatment, and post-treatment) throughout the treatment course. The dataset can serve a wide array of research projects including (but not limited to): quantitative imaging assessment, investigation on anatomical changes with treatment progress, dosimetry of target volumes and/or normal structures due to anatomical changes occurring during treatment, investigation of RT toxicity, and concurrent chemotherapy and RT effects on head-and-neck patients.

Evaluating the Use of rCBV as a Tumor Grade and Treatment Response Classifier Across NCI Quantitative Imaging Network Sites: Part II of the DSC-MRI Digital Reference Object (DRO) Challenge

  • Bell, Laura C
  • Semmineh, Natenael
  • An, Hongyu
  • Eldeniz, Cihat
  • Wahl, Richard
  • Schmainda, Kathleen M
  • Prah, Melissa A
  • Erickson, Bradley J
  • Korfiatis, Panagiotis
  • Wu, Chengyue
  • Sorace, Anna G
  • Yankeelov, Thomas E
  • Rutledge, Neal
  • Chenevert, Thomas L
  • Malyarenko, Dariya
  • Liu, Yichu
  • Brenner, Andrew
  • Hu, Leland S
  • Zhou, Yuxiang
  • Boxerman, Jerrold L
  • Yen, Yi-Fen
  • Kalpathy-Cramer, Jayashree
  • Beers, Andrew L
  • Muzi, Mark
  • Madhuranthakam, Ananth J
  • Pinho, Marco
  • Johnson, Brian
  • Quarles, C Chad
Tomography 2020 Journal Article, cited 1 times
Website
We have previously characterized the reproducibility of brain tumor relative cerebral blood volume (rCBV) using a dynamic susceptibility contrast magnetic resonance imaging digital reference object across 12 sites using a range of imaging protocols and software platforms. As expected, reproducibility was highest when imaging protocols and software were consistent, but decreased when they were variable. Our goal in this study was to determine the impact of rCBV reproducibility for tumor grade and treatment response classification. We found that varying imaging protocols and software platforms produced a range of optimal thresholds for both tumor grading and treatment response, but the performance of these thresholds was similar. These findings further underscore the importance of standardizing acquisition and analysis protocols across sites and software benchmarking.

Analysis of postprocessing steps for residue function dependent dynamic susceptibility contrast (DSC)‐MRI biomarkers and their clinical impact on glioma grading for both 1.5 and 3T

  • Bell, Laura C
  • Stokes, Ashley M
  • Quarles, C. Chad
Journal of Magnetic Resonance Imaging 2019 Journal Article, cited 0 times
Website
BACKGROUND: Dynamic susceptibility contrast (DSC)-MRI analysis pipelines differ across studies and sites, potentially confounding the clinical value and use of the derived biomarkers. PURPOSE/HYPOTHESIS: To investigate how postprocessing steps for computation of cerebral blood volume (CBV) and residue function dependent parameters (cerebral blood flow [CBF], mean transit time [MTT], capillary transit heterogeneity [CTH]) impact glioma grading. STUDY TYPE: Retrospective study from The Cancer Imaging Archive (TCIA). POPULATION: Forty-nine subjects with low- and high-grade gliomas. FIELD STRENGTH/SEQUENCE: 1.5 and 3.0T clinical systems using a single-echo echo planar imaging (EPI) acquisition. ASSESSMENT: Manual regions of interest (ROIs) were provided by TCIA and automatically segmented ROIs were generated by k-means clustering. CBV was calculated based on conventional equations. Residue function dependent biomarkers (CBF, MTT, CTH) were found by two deconvolution methods: circular discretization followed by a signal-to-noise ratio (SNR)-adapted eigenvalue thresholding (Method 1) and Volterra discretization with L-curve-based Tikhonov regularization (Method 2). STATISTICAL TESTS: Analysis of variance, receiver operating characteristics (ROC), and logistic regression tests. RESULTS: MTT alone was unable to statistically differentiate glioma grade (P > 0.139). When normalized, tumor CBF, CTH, and CBV did not differ across field strengths (P > 0.141). Biomarkers normalized to automatically segmented regions performed equally (rCTH AUROC is 0.73 compared with 0.74) or better (rCBF AUROC increases from 0.74-0.84; rCBV AUROC increases 0.78-0.86) than manually drawn ROIs. By updating the current deconvolution steps (Method 2), rCTH can act as a classifier for glioma grade (P < 0.007), but not if processed by current conventional DSC methods (Method 1) (P > 0.577). Lastly, higher-order biomarkers (eg, rCBF and rCTH) along with rCBV increases AUROC to 0.92 for differentiating tumor grade as compared with 0.78 and 0.86 (manual and automatic reference regions, respectively) for rCBV alone. DATA CONCLUSION: With optimized analysis pipelines, higher-order perfusion biomarkers (rCBF and rCTH) improve glioma grading as compared with CBV alone. Additionally, postprocessing steps impact thresholds needed for glioma grading. LEVEL OF EVIDENCE: 3 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2019.

Analysis of postprocessing steps for residue function dependent dynamic susceptibility contrast (DSC)‐MRI biomarkers and their clinical impact on glioma grading for both 1.5 and 3T

  • Bell, Laura C
  • Stokes, Ashley M
  • Quarles, C Chad
Journal of Magnetic Resonance Imaging 2020 Journal Article, cited 0 times
Website

Prostate Cancer Delineation in MRI Images Based on Deep Learning: Quantitative Comparison and Promising Perspective

  • Ben Loussaief, Eddardaa
  • Abdel-Nasser, Mohamed
  • Puig, Domènec
2021 Conference Paper, cited 0 times
Prostate cancer is the most common malignant male tumor. Magnetic Resonance Imaging (MRI) plays a crucial role in the detection, diagnosis, and treatment of prostate cancer diseases. Computer-aided diagnosis systems can help doctors to analyze MRI images and detect prostate cancer earlier. One of the key stages of prostate cancer CAD systems is the automatic delineation of the prostate. Deep learning has recently demonstrated promising segmentation results with medical images. The purpose of this paper is to compare the state-of-the-art of deep learning-based approaches for prostate delineation in MRI images and discussing their limitations and strengths. Besides, we introduce a promising perspective for prostate tumor classification in MRI images. This perspective includes the use of the best segmentation model to detect the prostate tumors in MRI images. Then, we will employ the segmented images to extract the radiomics features that will be used to discriminate benign or malignant prostate tumors.

Automatic Design of Window Operators for the Segmentation of the Prostate Gland in Magnetic Resonance Images

  • Benalcázar, Marco E
  • Brun, Marcel
  • Ballarin, Virginia
2015 Conference Proceedings, cited 0 times
Website

Overview of the American Society for Radiation Oncology–National Institutes of Health–American Association of Physicists in Medicine Workshop 2015: Exploring Opportunities for Radiation Oncology in the Era of Big Data

  • Benedict, Stanley H
  • Hoffman, Karen
  • Martel, Mary K
  • Abernethy, Amy P
  • Asher, Anthony L
  • Capala, Jacek
  • Chen, Ronald C
  • Chera, Bhisham
  • Couch, Jennifer
  • Deye, James
International Journal of Radiation Oncology• Biology• Physics 2016 Journal Article, cited 0 times

Segmentation of three-dimensional images with parametric active surfaces and topology changes

  • Benninghoff, Heike
  • Garcke, Harald
Journal of Scientific ComputingJ Sci Comput 2017 Journal Article, cited 1 times
Website
In this paper, we introduce a novel parametric finite element method for segmentation of three-dimensional images. We consider a piecewise constant version of the Mumford-Shah and the Chan-Vese functionals and perform a region-based segmentation of 3D image data. An evolution law is derived from energy minimization problems which push the surfaces to the boundaries of 3D objects in the image. We propose a parametric scheme which describes the evolution of parametric surfaces. An efficient finite element scheme is proposed for a numerical approximation of the evolution equations. Since standard parametric methods cannot handle topology changes automatically, an efficient method is presented to detect, identify and perform changes in the topology of the surfaces. One main focus of this paper are the algorithmic details to handle topology changes like splitting and merging of surfaces and change of the genus of a surface. Different artificial images are studied to demonstrate the ability to detect the different types of topology changes. Finally, the parametric method is applied to segmentation of medical 3D images.

Adverse prognosis of glioblastoma contacting the subventricular zone: Biological correlates

  • Berendsen, S.
  • van Bodegraven, E.
  • Seute, T.
  • Spliet, W. G. M.
  • Geurts, M.
  • Hendrikse, J.
  • Schoysman, L.
  • Huiszoon, W. B.
  • Varkila, M.
  • Rouss, S.
  • Bell, E. H.
  • Kroonen, J.
  • Chakravarti, A.
  • Bours, V.
  • Snijders, T. J.
  • Robe, P. A.
PLoS One 2019 Journal Article, cited 2 times
Website
INTRODUCTION: The subventricular zone (SVZ) in the brain is associated with gliomagenesis and resistance to treatment in glioblastoma. In this study, we investigate the prognostic role and biological characteristics of subventricular zone (SVZ) involvement in glioblastoma. METHODS: We analyzed T1-weighted, gadolinium-enhanced MR images of a retrospective cohort of 647 primary glioblastoma patients diagnosed between 2005-2013, and performed a multivariable Cox regression analysis to adjust the prognostic effect of SVZ involvement for clinical patient- and tumor-related factors. Protein expression patterns of a.o. markers of neural stem cellness (CD133 and GFAP-delta) and (epithelial-) mesenchymal transition (NF-kappaB, C/EBP-beta and STAT3) were determined with immunohistochemistry on tissue microarrays containing 220 of the tumors. Molecular classification and mRNA expression-based gene set enrichment analyses, miRNA expression and SNP copy number analyses were performed on fresh frozen tissue obtained from 76 tumors. Confirmatory analyses were performed on glioblastoma TCGA/TCIA data. RESULTS: Involvement of the SVZ was a significant adverse prognostic factor in glioblastoma, independent of age, KPS, surgery type and postoperative treatment. Tumor volume and postoperative complications did not explain this prognostic effect. SVZ contact was associated with increased nuclear expression of the (epithelial-) mesenchymal transition markers C/EBP-beta and phospho-STAT3. SVZ contact was not associated with molecular subtype, distinct gene expression patterns, or markers of stem cellness. Our main findings were confirmed in a cohort of 229 TCGA/TCIA glioblastomas. CONCLUSION: In conclusion, involvement of the SVZ is an independent prognostic factor in glioblastoma, and associates with increased expression of key markers of (epithelial-) mesenchymal transformation, but does not correlate with stem cellness, molecular subtype, or specific (mi)RNA expression patterns.

Pulmonary nodule detection using a cascaded SVM classifier

  • Bergtholdt, Martin
  • Wiemker, Rafael
  • Klinder, Tobias
2016 Conference Proceedings, cited 9 times
Website
Automatic detection of lung nodules from chest CT has been researched intensively over the last decades resulting also in several commercial products. However, solutions are adopted only slowly into daily clinical routine as many current CAD systems still potentially miss true nodules while at the same time generating too many false positives (FP). While many earlier approaches had to rely on rather few cases for development, larger databases become now available and can be used for algorithmic development. In this paper, we address the problem of lung nodule detection via a cascaded SVM classifier. The idea is to sequentially perform two classification tasks in order to select from an extremely large pool of potential candidates the few most likely ones. As the initial pool is allowed to contain thousands of candidates, very loose criteria could be applied during this pre-selection. In this way, the chances that a true nodule is falsely rejected as a candidate are reduced significantly. The final algorithm is trained and tested on the full LIDC/IDRI database. Comparison is done against two previously published CAD systems. Overall, the algorithm achieved sensitivity of 0.859 at 2.5 FP/volume where the other two achieved sensitivity values of 0.321 and 0.625, respectively. On low dose data sets, only slight increase in the number of FP/volume was observed, while the sensitivity was not affected.

Detection of Motion Artifacts in Thoracic CT Scans

  • Beri, Puneet S.
2020 Thesis, cited 0 times
Website
The analysis of a lung CT scan can be a complicated task due to the presence of certain image artifacts such as cardiac motion, respiratory motion, beam hardening artefacts, and so on. In this project, we have built a deep learning based model for the detection of these motion artifacts in the image. Using biomedical image segmentation models we have trained the model on lung CT scans from the LIDC dataset. The developed model is able to identify the regions in the scan which are affected by motion by segmenting the image. Further it is also able to separate normal (or easy to analyze) CT scans from CT scans that may provide incorrect quantitative analysis, even when the examples of image artifacts or low quality scans are scarce. In addition, the model is able to evaluate a quality score for the scan based on the amount of artifacts detected which could hamper its authenticity for the further diagnosisof disease or disease progression. We used two main approaches during the experimentation process - 2D slice based approaches and 2D patch based approaches of which the patch based approaches yielded the final model. The final model gave an AUC of 0.814 in the ROC analysis of the evaluation study conducted. Discussions on the approaches and findings of the final model are provided and future directions are proposed.

Optimizing Convolutional Neural Network by Hybridized Elephant Herding Optimization Algorithm for Magnetic Resonance Image Classification of Glioma Brain Tumor Grade

  • Timea Bezdan
  • Stefan Milosevic
  • K Venkatachalam
  • Miodrag Zivkovic
  • Nebojsa Bacanin
  • Ivana Strumberger
2021 Conference Paper, cited 0 times
Website
Gliomas belong to the group of the most frequent types of brain tumors. For this specific type of brain tumors, in its beginning stages, it is extremely complex to get the exact diagnosis. Even with the works from the most experienced doctors, it will not be possible without magnetic resonance imaging, which aids to make the diagnosis of brain tumors. In order to create classification of the images, to where the class of glioma belongs to, for achieving superior performance, convolutional neural networks can be used. For achieving high-level accuracy on the image classification, the convolutional network hyperparameters’ calibrations must reach a very accurate response of high accuracy results and this task proves to take up a lot of computational time and energy. Proceeding with the proposed solution, in this scientific research paper a metaheuristic method has been proposed to automatically search and target the near-optimal values of convolutional neural network hyperparameters based on hybridized version of elephant herding optimization swarm intelligence metaheuristics. The hybridized elephant herding optimization has been incorporated for convolutional neural network hyperparameters’ tuning to develop a system for automatic and instantaneous image classification of glioma brain tumors grades from the magnetic resonance imaging. Comparative analysis was performed with other methods tested on the same problem instance an results proved superiority of approach proposed in this paper.

Fuzzy volumetric delineation of brain tumor and survival prediction

  • Bhadani, Saumya
  • Mitra, Sushmita
  • Banerjee, Subhashis
Soft Computing 2020 Journal Article, cited 0 times
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A novel three-dimensional detailed delineation algorithm is introduced for Glioblastoma multiforme tumors in MRI. It efficiently delineates the whole tumor, enhancing core, edema and necrosis volumes using fuzzy connectivity and multi-thresholding, based on a single seed voxel. While the whole tumor volume delineation uses FLAIR and T2 MRI channels, the outlining of the enhancing core, necrosis and edema volumes employs the T1C channel. Discrete curve evolution is initially applied for multi-thresholding, to determine intervals around significant (visually critical) points, and a threshold is determined in each interval using bi-level Otsu’s method or Li and Lee’s entropy. This is followed by an interactive whole tumor volume delineation using FLAIR and T2 MRI sequences, requiring a single user-defined seed. An efficient and robust whole tumor extraction is executed using fuzzy connectedness and dynamic thresholding. Finally, the segmented whole tumor volume in T1C MRI channel is again subjected to multi-level segmentation, to delineate its sub-parts, encompassing enhancing core, necrosis and edema. This was followed by survival prediction of patients using the concept of habitats. Qualitative and quantitative evaluation, on FLAIR, T2 and T1C MR sequences of 29 GBM patients, establish its superiority over related methods, visually as well as in terms of Dice scores, Sensitivity and Hausdorff distance.

Deep-learning framework to detect lung abnormality – A study with chest X-Ray and lung CT scan images

  • Bhandary, Abhir
  • Prabhu, G. Ananth
  • Rajinikanth, V.
  • Thanaraj, K. Palani
  • Satapathy, Suresh Chandra
  • Robbins, David E.
  • Shasky, Charles
  • Zhang, Yu-Dong
  • Tavares, João Manuel R. S.
  • Raja, N. Sri Madhava
Pattern Recognition Letters 2020 Journal Article, cited 0 times
Website
Lung abnormalities are highly risky conditions in humans. The early diagnosis of lung abnormalities is essential to reduce the risk by enabling quick and efficient treatment. This research work aims to propose a Deep-Learning (DL) framework to examine lung pneumonia and cancer. This work proposes two different DL techniques to assess the considered problem: (i) The initial DL method, named a modified AlexNet (MAN), is proposed to classify chest X-Ray images into normal and pneumonia class. In the MAN, the classification is implemented using with Support Vector Machine (SVM), and its performance is compared against Softmax. Further, its performance is validated with other pre-trained DL techniques, such as AlexNet, VGG16, VGG19 and ResNet50. (ii) The second DL work implements a fusion of handcrafted and learned features in the MAN to improve classification accuracy during lung cancer assessment. This work employs serial fusion and Principal Component Analysis (PCA) based features selection to enhance the feature vector. The performance of this DL frame work is tested using benchmark lung cancer CT images of LIDC-IDRI and classification accuracy (97.27%) is attained.

Radial Cumulative Frequency Distribution: A New Imaging Signature to Detect Chromosomal Arms 1p/19q Co-deletion Status in Glioma

  • Debanjali Bhattacharya
  • Neelam Sinha
  • Jitender Saini
2020 Conference Proceedings, cited 0 times
Website
Gliomas are the most common primary brain tumor and are associated with high mortality. Gene mutations are one of the hallmarks of glioma formation, determining its aggressiveness as well as patients’s response towards treatment. The paper presents a novel approach to detect chromosomal arms 1p/19q co-deletion status non-invasively in low-graded glioma based on its textural characteristics in frequency domain. For this, we derived Radial Cumulative Frequency Distribution (RCFD) function from Fourier power spectrum of consecutive glioma slices. Multi-parametric MRIs of 159 grade-2 and grade-3 glioma patients, having biopsy proven 1p/19q mutational status (non-deletion: n = 57 and co-deletion: n = 102) was used in this study. Different RCFD textural features were extracted to quantify MRI image signature pattern of mutant and wildtype glioma. Owing to skewed dataset we have performed RUSBoost classification; yielding average accuracy of 73.5% for grade-2 and 83% for grade-3 glioma subjects. The efficacy of the proposed technique is discussed further in comparison with state-of-art methods.

Isolation of Prostate Gland in T1-Weighted Magnetic Resonance Images using Computer Vision

  • Bhattacharya, Sayantan
  • Sharma, Apoorv
  • Gupta, Rinki
  • Bhan, Anupama
2020 Conference Proceedings, cited 0 times
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G-DOC Plus–an integrative bioinformatics platform for precision medicine

  • Bhuvaneshwar, Krithika
  • Belouali, Anas
  • Singh, Varun
  • Johnson, Robert M
  • Song, Lei
  • Alaoui, Adil
  • Harris, Michael A
  • Clarke, Robert
  • Weiner, Louis M
  • Gusev, Yuriy
BMC Bioinformatics 2016 Journal Article, cited 14 times
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Artificial intelligence in cancer imaging: Clinical challenges and applications

  • Bi, Wenya Linda
  • Hosny, Ahmed
  • Schabath, Matthew B
  • Giger, Maryellen L
  • Birkbak, Nicolai J
  • Mehrtash, Alireza
  • Allison, Tavis
  • Arnaout, Omar
  • Abbosh, Christopher
  • Dunn, Ian F
CA: a cancer journal for clinicians 2019 Journal Article, cited 0 times
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A comparison of ground truth estimation methods

  • Biancardi, Alberto M
  • Jirapatnakul, Artit C
  • Reeves, Anthony P
International Journal of Computer Assisted Radiology and Surgery 2010 Journal Article, cited 17 times
Website
PURPOSE: Knowledge of the exact shape of a lesion, or ground truth (GT), is necessary for the development of diagnostic tools by means of algorithm validation, measurement metric analysis, accurate size estimation. Four methods that estimate GTs from multiple readers' documentations by considering the spatial location of voxels were compared: thresholded Probability-Map at 0.50 (TPM(0.50)) and at 0.75 (TPM(0.75)), simultaneous truth and performance level estimation (STAPLE) and truth estimate from self distances (TESD). METHODS: A subset of the publicly available Lung Image Database Consortium archive was used, selecting pulmonary nodules documented by all four radiologists. The pair-wise similarities between the estimated GTs were analyzed by computing the respective Jaccard coefficients. Then, with respect to the readers' marking volumes, the estimated volumes were ranked and the sign test of the differences between them was performed. RESULTS: (a) the rank variations among the four methods and the volume differences between STAPLE and TESD are not statistically significant, (b) TPM(0.50) estimates are statistically larger (c) TPM(0.75) estimates are statistically smaller (d) there is some spatial disagreement in the estimates as the one-sided 90% confidence intervals between TPM(0.75) and TPM(0.50), TPM(0.75) and STAPLE, TPM(0.75) and TESD, TPM(0.50) and STAPLE, TPM(0.50) and TESD, STAPLE and TESD, respectively, show: [0.67, 1.00], [0.67, 1.00], [0.77, 1.00], [0.93, 1.00], [0.85, 1.00], [0.85, 1.00]. CONCLUSIONS: The method used to estimate the GT is important: the differences highlighted that STAPLE and TESD, notwithstanding a few weaknesses, appear to be equally viable as a GT estimator, while the increased availability of computing power is decreasing the appeal afforded to TPMs. Ultimately, the choice of which GT estimation method, between the two, should be preferred depends on the specific characteristics of the marked data that is used with respect to the two elements that differentiate the method approaches: relative reliabilities of the readers and the reliability of the region boundaries.

Comparative evaluation of conventional and deep learning methods for semi-automated segmentation of pulmonary nodules on CT

  • Bianconi, Francesco
  • Fravolini, Mario Luca
  • Pizzoli, Sofia
  • Palumbo, Isabella
  • Minestrini, Matteo
  • Rondini, Maria
  • Nuvoli, Susanna
  • Spanu, Angela
  • Palumbo, Barbara
Quant Imaging Med Surg 2021 Journal Article, cited 2 times
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Background: Accurate segmentation of pulmonary nodules on computed tomography (CT) scans plays a crucial role in the evaluation and management of patients with suspicion of lung cancer (LC). When performed manually, not only the process requires highly skilled operators, but is also tiresome and time-consuming. To assist the physician in this task several automated and semi-automated methods have been proposed in the literature. In recent years, in particular, the appearance of deep learning has brought about major advances in the field. Methods: Twenty-four (12 conventional and 12 based on deep learning) semi-automated-'one-click'-methods for segmenting pulmonary nodules on CT were evaluated in this study. The experiments were carried out on two datasets: a proprietary one (383 images from a cohort of 111 patients) and a public one (259 images from a cohort of 100). All the patients had a positive transcript for suspect pulmonary nodules. Results: The methods based on deep learning clearly outperformed the conventional ones. The best performance [Sorensen-Dice coefficient (DSC)] in the two datasets was, respectively, 0.853 and 0.763 for the deep learning methods, and 0.761 and 0.704 for the traditional ones. Conclusions: Deep learning is a viable approach for semi-automated segmentation of pulmonary nodules on CT scans.

Convolutional neural networks for head and neck tumor segmentation on 7-channel multiparametric MRI: a leave-one-out analysis

  • Bielak, Lars
  • Wiedenmann, Nicole
  • Berlin, Arnie
  • Nicolay, Nils Henrik
  • Gunashekar, Deepa Darshini
  • Hagele, Leonard
  • Lottner, Thomas
  • Grosu, Anca-Ligia
  • Bock, Michael
Radiat Oncol 2020 Journal Article, cited 1 times
Website
BACKGROUND: Automatic tumor segmentation based on Convolutional Neural Networks (CNNs) has shown to be a valuable tool in treatment planning and clinical decision making. We investigate the influence of 7 MRI input channels of a CNN with respect to the segmentation performance of head&neck cancer. METHODS: Head&neck cancer patients underwent multi-parametric MRI including T2w, pre- and post-contrast T1w, T2*, perfusion (ktrans, ve) and diffusion (ADC) measurements at 3 time points before and during radiochemotherapy. The 7 different MRI contrasts (input channels) and manually defined gross tumor volumes (primary tumor and lymph node metastases) were used to train CNNs for lesion segmentation. A reference CNN with all input channels was compared to individually trained CNNs where one of the input channels was left out to identify which MRI contrast contributes the most to the tumor segmentation task. A statistical analysis was employed to account for random fluctuations in the segmentation performance. RESULTS: The CNN segmentation performance scored up to a Dice similarity coefficient (DSC) of 0.65. The network trained without T2* data generally yielded the worst results, with DeltaDSCGTV-T = 5.7% for primary tumor and DeltaDSCGTV-Ln = 5.8% for lymph node metastases compared to the network containing all input channels. Overall, the ADC input channel showed the least impact on segmentation performance, with DeltaDSCGTV-T = 2.4% for primary tumor and DeltaDSCGTV-Ln = 2.2% respectively. CONCLUSIONS: We developed a method to reduce overall scan times in MRI protocols by prioritizing those sequences that add most unique information for the task of automatic tumor segmentation. The optimized CNNs could be used to aid in the definition of the GTVs in radiotherapy planning, and the faster imaging protocols will reduce patient scan times which can increase patient compliance. TRIAL REGISTRATION: The trial was registered retrospectively at the German Register for Clinical Studies (DRKS) under register number DRKS00003830 on August 20th, 2015.

Learning to detect anatomical landmarks of the pelvis in X-rays from arbitrary views

  • Bier, B.
  • Goldmann, F.
  • Zaech, J. N.
  • Fotouhi, J.
  • Hegeman, R.
  • Grupp, R.
  • Armand, M.
  • Osgood, G.
  • Navab, N.
  • Maier, A.
  • Unberath, M.
Int J Comput Assist Radiol Surg 2019 Journal Article, cited 0 times
Website
Purpose Minimally invasive alternatives are now available for many complex surgeries. These approaches are enabled by the increasing availability of intra-operative image guidance. Yet, fluoroscopic X-rays suffer from projective transformation and thus cannot provide direct views onto anatomy. Surgeons could highly benefit from additional information, such as the anatomical landmark locations in the projections, to support intra-operative decision making. However, detecting landmarks is challenging since the viewing direction changes substantially between views leading to varying appearance of the same landmark. Therefore, and to the best of our knowledge, view-independent anatomical landmark detection has not been investigated yet. Methods In this work, we propose a novel approach to detect multiple anatomical landmarks in X-ray images from arbitrary viewing directions. To this end, a sequential prediction framework based on convolutional neural networks is employed to simultaneously regress all landmark locations. For training, synthetic X-rays are generated with a physically accurate forward model that allows direct application of the trained model to real X-ray images of the pelvis. View invariance is achieved via data augmentation by sampling viewing angles on a spherical segment of 120∘×90∘ . Results On synthetic data, a mean prediction error of 5.6 ± 4.5 mm is achieved. Further, we demonstrate that the trained model can be directly applied to real X-rays and show that these detections define correspondences to a respective CT volume, which allows for analytic estimation of the 11 degree of freedom projective mapping. Conclusion We present the first tool to detect anatomical landmarks in X-ray images independent of their viewing direction. Access to this information during surgery may benefit decision making and constitutes a first step toward global initialization of 2D/3D registration without the need of calibration. As such, the proposed concept has a strong prospect to facilitate and enhance applications and methods in the realm of image-guided surgery.

Multiparametric MRI and auto-fixed volume of interest-based radiomics signature for clinically significant peripheral zone prostate cancer

  • Bleker, J.
  • Kwee, T. C.
  • Dierckx, Rajo
  • de Jong, I. J.
  • Huisman, H.
  • Yakar, D.
Eur Radiol 2020 Journal Article, cited 2 times
Website
OBJECTIVES: To create a radiomics approach based on multiparametric magnetic resonance imaging (mpMRI) features extracted from an auto-fixed volume of interest (VOI) that quantifies the phenotype of clinically significant (CS) peripheral zone (PZ) prostate cancer (PCa). METHODS: This study included 206 patients with 262 prospectively called mpMRI prostate imaging reporting and data system 3-5 PZ lesions. Gleason scores > 6 were defined as CS PCa. Features were extracted with an auto-fixed 12-mm spherical VOI placed around a pin point in each lesion. The value of dynamic contrast-enhanced imaging(DCE), multivariate feature selection and extreme gradient boosting (XGB) vs. univariate feature selection and random forest (RF), expert-based feature pre-selection, and the addition of image filters was investigated using the training (171 lesions) and test (91 lesions) datasets. RESULTS: The best model with features from T2-weighted (T2-w) + diffusion-weighted imaging (DWI) + DCE had an area under the curve (AUC) of 0.870 (95% CI 0.980-0.754). Removal of DCE features decreased AUC to 0.816 (95% CI 0.920-0.710), although not significantly (p = 0.119). Multivariate and XGB outperformed univariate and RF (p = 0.028). Expert-based feature pre-selection and image filters had no significant contribution. CONCLUSIONS: The phenotype of CS PZ PCa lesions can be quantified using a radiomics approach based on features extracted from T2-w + DWI using an auto-fixed VOI. Although DCE features improve diagnostic performance, this is not statistically significant. Multivariate feature selection and XGB should be preferred over univariate feature selection and RF. The developed model may be a valuable addition to traditional visual assessment in diagnosing CS PZ PCa. KEY POINTS: * T2-weighted and diffusion-weighted imaging features are essential components of a radiomics model for clinically significant prostate cancer; addition of dynamic contrast-enhanced imaging does not significantly improve diagnostic performance. * Multivariate feature selection and extreme gradient outperform univariate feature selection and random forest. * The developed radiomics model that extracts multiparametric MRI features with an auto-fixed volume of interest may be a valuable addition to visual assessment in diagnosing clinically significant prostate cancer.

Harnessing multimodal data integration to advance precision oncology

  • Boehm, Kevin M.
  • Khosravi, Pegah
  • Vanguri, Rami
  • Gao, Jianjiong
  • Shah, Sohrab P.
Nature Reviews Cancer 2021 Journal Article, cited 0 times
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Advances in quantitative biomarker development have accelerated new forms of data-driven insights for patients with cancer. However, most approaches are limited to a single mode of data, leaving integrated approaches across modalities relatively underdeveloped. Multimodal integration of advanced molecular diagnostics, radiological and histological imaging, and codified clinical data presents opportunities to advance precision oncology beyond genomics and standard molecular techniques. However, most medical datasets are still too sparse to be useful for the training of modern machine learning techniques, and significant challenges remain before this is remedied. Combined efforts of data engineering, computational methods for analysis of heterogeneous data and instantiation of synergistic data models in biomedical research are required for success. In this Perspective, we offer our opinions on synthesizing complementary modalities of data with emerging multimodal artificial intelligence methods. Advancing along this direction will result in a reimagined class of multimodal biomarkers to propel the field of precision oncology in the coming decade.

Dynamic conformal arcs for lung stereotactic body radiation therapy: A comparison with volumetric-modulated arc therapy

  • Bokrantz, R.
  • Wedenberg, M.
  • Sandwall, P.
J Appl Clin Med Phys 2020 Journal Article, cited 1 times
Website
This study constitutes a feasibility assessment of dynamic conformal arc (DCA) therapy as an alternative to volumetric-modulated arc therapy (VMAT) for stereotactic body radiation therapy (SBRT) of lung cancer. The rationale for DCA is lower geometric complexity and hence reduced risk for interplay errors induced by respiratory motion. Forward planned DCA and inverse planned DCA based on segment-weight optimization were compared to VMAT for single arc treatments of five lung patients. Analysis of dose-volume histograms and clinical goal fulfillment revealed that DCA can generate satisfactory and near equivalent dosimetric quality to VMAT, except for complex tumor geometries. Segment-weight optimized DCA provided spatial dose distributions qualitatively similar to those for VMAT. Our results show that DCA, and particularly segment-weight optimized DCA, may be an attractive alternative to VMAT for lung SBRT treatments if the patient anatomy is favorable.

Integration of convolutional neural networks for pulmonary nodule malignancy assessment in a lung cancer classification pipeline

  • Bonavita, I.
  • Rafael-Palou, X.
  • Ceresa, M.
  • Piella, G.
  • Ribas, V.
  • Gonzalez Ballester, M. A.
Comput Methods Programs Biomed 2020 Journal Article, cited 3 times
Website
BACKGROUND AND OBJECTIVE: The early identification of malignant pulmonary nodules is critical for a better lung cancer prognosis and less invasive chemo or radio therapies. Nodule malignancy assessment done by radiologists is extremely useful for planning a preventive intervention but is, unfortunately, a complex, time-consuming and error-prone task. This explains the lack of large datasets containing radiologists malignancy characterization of nodules; METHODS: In this article, we propose to assess nodule malignancy through 3D convolutional neural networks and to integrate it in an automated end-to-end existing pipeline of lung cancer detection. For training and testing purposes we used independent subsets of the LIDC dataset; RESULTS: Adding the probabilities of nodules malignity in a baseline lung cancer pipeline improved its F1-weighted score by 14.7%, whereas integrating the malignancy model itself using transfer learning outperformed the baseline prediction by 11.8% of F1-weighted score; CONCLUSIONS: Despite the limited size of the lung cancer datasets, integrating predictive models of nodule malignancy improves prediction of lung cancer.

CT Colonography: External Clinical Validation of an Algorithm for Computer-assisted Prone and Supine Registration

  • Boone, Darren J
  • Halligan, Steve
  • Roth, Holger R
  • Hampshire, Tom E
  • Helbren, Emma
  • Slabaugh, Greg G
  • McQuillan, Justine
  • McClelland, Jamie R
  • Hu, Mingxing
  • Punwani, Shonit
RadiologyRadiology 2013 Journal Article, cited 5 times
Website
PURPOSE: To perform external validation of a computer-assisted registration algorithm for prone and supine computed tomographic (CT) colonography and to compare the results with those of an existing centerline method. MATERIALS AND METHODS: All contributing centers had institutional review board approval; participants provided informed consent. A validation sample of CT colonographic examinations of 51 patients with 68 polyps (6-55 mm) was selected from a publicly available, HIPAA compliant, anonymized archive. No patients were excluded because of poor preparation or inadequate distension. Corresponding prone and supine polyp coordinates were recorded, and endoluminal surfaces were registered automatically by using a computer algorithm. Two observers independently scored three-dimensional endoluminal polyp registration success. Results were compared with those obtained by using the normalized distance along the colonic centerline (NDACC) method. Pairwise Wilcoxon signed rank tests were used to compare gross registration error and McNemar tests were used to compare polyp conspicuity. RESULTS: Registration was possible in all 51 patients, and 136 paired polyp coordinates were generated (68 polyps) to test the algorithm. Overall mean three-dimensional polyp registration error (mean +/- standard deviation, 19.9 mm +/- 20.4) was significantly less than that for the NDACC method (mean, 27.4 mm +/- 15.1; P = .001). Accuracy was unaffected by colonic segment (P = .76) or luminal collapse (P = .066). During endoluminal review by two observers (272 matching tasks, 68 polyps, prone to supine and supine to prone coordinates), 223 (82%) polyp matches were visible (120 degrees field of view) compared with just 129 (47%) when the NDACC method was used (P < .001). By using multiplanar visualization, 48 (70%) polyps were visible after scrolling +/- 15 mm in any multiplanar axis compared with 16 (24%) for NDACC (P < .001). CONCLUSION: Computer-assisted registration is more accurate than the NDACC method for mapping the endoluminal surface and matching the location of polyps in corresponding prone and supine CT colonographic acquisitions.

Solid Indeterminate Nodules with a Radiological Stability Suggesting Benignity: A Texture Analysis of Computed Tomography Images Based on the Kurtosis and Skewness of the Nodule Volume Density Histogram

  • Borguezan, Bruno Max
  • Lopes, Agnaldo José
  • Saito, Eduardo Haruo
  • Higa, Claudio
  • Silva, Aristófanes Corrêa
  • Nunes, Rodolfo Acatauassú
Pulmonary Medicine 2019 Journal Article, cited 0 times
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BACKGROUND: The number of incidental findings of pulmonary nodules using imaging methods to diagnose other thoracic or extrathoracic conditions has increased, suggesting the need for in-depth radiological image analyses to identify nodule type and avoid unnecessary invasive procedures. OBJECTIVES:The present study evaluated solid indeterminate nodules with a radiological stability suggesting benignity (SINRSBs) through a texture analysis of computed tomography (CT) images. METHODS: A total of 100 chest CT scans were evaluated, including 50 cases of SINRSBs and 50 cases of malignant nodules. SINRSB CT scans were performed using the same noncontrast enhanced CT protocol and equipment; the malignant nodule data were acquired from several databases. The kurtosis (KUR) and skewness (SKW) values of these tests were determined for the whole volume of each nodule, and the histograms were classified into two basic patterns: peaks or plateaus. RESULTS: The mean (MEN) KUR values of the SINRSBs and malignant nodules were 3.37 ± 3.88 and 5.88 ± 5.11, respectively. The receiver operating characteristic (ROC) curve showed that the sensitivity and specificity for distinguishing SINRSBs from malignant nodules were 65% and 66% for KUR values >6, respectively, with an area under the curve (AUC) of 0.709 (p< 0.0001). The MEN SKW values of the SINRSBs and malignant nodules were 1.73 ± 0.94 and 2.07 ± 1.01, respectively. The ROC curve showed that the sensitivity and specificity for distinguishing malignant nodules from SINRSBs were 65% and 66% for SKW values >3.1, respectively, with an AUC of 0.709 (p < 0.0001). An analysis of the peak and plateau histograms revealed sensitivity, specificity, and accuracy values of 84%, 74%, and 79%, respectively. CONCLUSION: KUR, SKW, and histogram shape can help to noninvasively diagnose SINRSBs but should not be used alone or without considering clinical data.

3D automatic levels propagation approach to breast MRI tumor segmentation

  • Bouchebbah, Fatah
  • Slimani, Hachem
Expert Systems with Applications 2020 Journal Article, cited 0 times
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Magnetic Resonance Imaging MRI is a relevant tool for breast cancer screening. Moreover, an accurate 3D segmentation of breast tumors from MRI scans plays a key role in the analysis of the disease. In this manuscript, we propose a novel 3D automatic method for segmenting MRI breast tumors, called 3D Automatic Levels Propagation Approach (3D-ALPA). The proposed method performs the segmentation automatically in two steps: in the first step, the entire MRI volume to process is segmented slice by slice. Specifically, using a new automatic approach called 2D Automatic Levels Propagation Approach (2D-ALPA) which is an improved version of a previous semi-automatic approach, named 2D Levels Propagation Approach (2D-LPA). In the second step, the partial segmentations obtained after the application of 2D-ALPA are recombined to rebuild the complete volume(s) of tumor(s). 3D-ALPA has many characteristics, mainly: it is an automatic method which can take into consideration multi-tumor segmentation, and it has the property to be easily applicable according to the Axial, Coronal, as well as Sagittal planes. Therefore, it offers a multi-view representation of the segmented tumor(s). To validate the new 3D-ALPA method, we have firstly performed tests on a 2D private dataset composed of eighteen patients to estimate the accuracy of the new 2D-ALPA in comparison to the previous 2D-LPA. The obtained results have been in favor of the proposed 2D-ALPA, showing hence an improvement in accuracy after integrating the automatization in the 2D-ALPA approach. Then, we have evaluated the complete 3D-ALPA method on a 3D private dataset constituted of MRI exams of twenty-two patients having real breast tumors of different types, and on the public RIDER dataset. Essentially, 3D-ALPA has been evaluated regarding two main features: segmentation accuracy and running time, by considering two kinds of breast tumors: non-enhanced and enhanced tumors. The experimental studies have shown that 3D-ALPA has produced better results for the both kinds of tumors than a recent and concurrent method in the literature that addresses the same problematic.

Radiogenomics of Clear Cell Renal Cell Carcinoma: Associations Between mRNA-Based Subtyping and CT Imaging Features

  • Bowen, Lan
  • Xiaojing, Li
Academic Radiology 2018 Journal Article, cited 0 times
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Singular value decomposition using block least mean square method for image denoising and compression

  • Boyat, Ajay Kumar
  • Khare, Parth
2015 Conference Proceedings, cited 1 times
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Association of Peritumoral Radiomics With Tumor Biology and Pathologic Response to Preoperative Targeted Therapy for HER2 (ERBB2)-Positive Breast Cancer

  • Braman, Nathaniel
  • Prasanna, Prateek
  • Whitney, Jon
  • Singh, Salendra
  • Beig, Niha
  • Etesami, Maryam
  • Bates, David D. B.
  • Gallagher, Katherine
  • Bloch, B. Nicolas
  • Vulchi, Manasa
  • Turk, Paulette
  • Bera, Kaustav
  • Abraham, Jame
  • Sikov, William M.
  • Somlo, George
  • Harris, Lyndsay N.
  • Gilmore, Hannah
  • Plecha, Donna
  • Varadan, Vinay
  • Madabhushi, Anant
JAMA Netw Open 2019 Journal Article, cited 0 times
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Importance There has been significant recent interest in understanding the utility of quantitative imaging to delineate breast cancer intrinsic biological factors and therapeutic response. No clinically accepted biomarkers are as yet available for estimation of response to human epidermal growth factor receptor 2 (currently known as ERBB2, but referred to as HER2 in this study)–targeted therapy in breast cancer. Objective To determine whether imaging signatures on clinical breast magnetic resonance imaging (MRI) could noninvasively characterize HER2-positive tumor biological factors and estimate response to HER2-targeted neoadjuvant therapy. Design, Setting, and Participants In a retrospective diagnostic study encompassing 209 patients with breast cancer, textural imaging features extracted within the tumor and annular peritumoral tissue regions on MRI were examined as a means to identify increasingly granular breast cancer subgroups relevant to therapeutic approach and response. First, among a cohort of 117 patients who received an MRI prior to neoadjuvant chemotherapy (NAC) at a single institution from April 27, 2012, through September 4, 2015, imaging features that distinguished HER2+ tumors from other receptor subtypes were identified. Next, among a cohort of 42 patients with HER2+ breast cancers with available MRI and RNaseq data accumulated from a multicenter, preoperative clinical trial (BrUOG 211B), a signature of the response-associated HER2-enriched (HER2-E) molecular subtype within HER2+ tumors (n = 42) was identified. The association of this signature with pathologic complete response was explored in 2 patient cohorts from different institutions, where all patients received HER2-targeted NAC (n = 28, n = 50). Finally, the association between significant peritumoral features and lymphocyte distribution was explored in patients within the BrUOG 211B trial who had corresponding biopsy hematoxylin-eosin–stained slide images. Data analysis was conducted from January 15, 2017, to February 14, 2019. Main Outcomes and Measures Evaluation of imaging signatures by the area under the receiver operating characteristic curve (AUC) in identifying HER2+ molecular subtypes and distinguishing pathologic complete response (ypT0/is) to NAC with HER2-targeting. Results In the 209 patients included (mean [SD] age, 51.1 [11.7] years), features from the peritumoral regions better discriminated HER2-E tumors (maximum AUC, 0.85; 95% CI, 0.79-0.90; 9-12 mm from the tumor) compared with intratumoral features (AUC, 0.76; 95% CI, 0.69-0.84). A classifier combining peritumoral and intratumoral features identified the HER2-E subtype (AUC, 0.89; 95% CI, 0.84-0.93) and was significantly associated with response to HER2-targeted therapy in both validation cohorts (AUC, 0.80; 95% CI, 0.61-0.98 and AUC, 0.69; 95% CI, 0.53-0.84). Features from the 0- to 3-mm peritumoral region were significantly associated with the density of tumor-infiltrating lymphocytes (R2 = 0.57; 95% CI, 0.39-0.75; P = .002). Conclusions and Relevance A combination of peritumoral and intratumoral characteristics appears to identify intrinsic molecular subtypes of HER2+ breast cancers from imaging, offering insights into immune response within the peritumoral environment and suggesting potential benefit for treatment guidance.

A volumetric technique for fossil body mass estimation applied to Australopithecus afarensis

  • Brassey, Charlotte A
  • O'Mahoney, Thomas G
  • Chamberlain, Andrew T
  • Sellers, William I
Journal of human evolution 2018 Journal Article, cited 3 times
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Constructing 3D-Printable CAD Models of Prostates from MR Images

  • Breseman, Kelsey
  • Lee, Christopher
  • Bloch, B Nicholas
  • Jaffe, Carl
2013 Conference Proceedings, cited 1 times
Website
This paper describes the development of a procedure to generate patient-specific, three-dimensional (3D) solid models of prostates (and related anatomy) from magnetic resonance (MR) images. The 3D models are rendered in STL file format which can be physically printed or visualized on a holographic display system. An example is presented in which a 3D model is printed following this procedure.

An ensemble learning approach for brain cancer detection exploiting radiomic features

  • Brunese, Luca
  • Mercaldo, Francesco
  • Reginelli, Alfonso
  • Santone, Antonella
Comput Methods Programs Biomed 2019 Journal Article, cited 1 times
Website
BACKGROUND AND OBJECTIVE: The brain cancer is one of the most aggressive tumour: the 70% of the patients diagnosed with this malignant cancer will not survive. Early detection of brain tumours can be fundamental to increase survival rates. The brain cancers are classified into four different grades (i.e., I, II, III and IV) according to how normal or abnormal the brain cells look. The following work aims to recognize the different brain cancer grades by analysing brain magnetic resonance images. METHODS: A method to identify the components of an ensemble learner is proposed. The ensemble learner is focused on the discrimination between different brain cancer grades using non invasive radiomic features. The considered radiomic features are belonging to five different groups: First Order, Shape, Gray Level Co-occurrence Matrix, Gray Level Run Length Matrix and Gray Level Size Zone Matrix. We evaluate the features effectiveness through hypothesis testing and through decision boundaries, performance analysis and calibration plots thus we select the best candidate classifiers for the ensemble learner. RESULTS: We evaluate the proposed method with 111,205 brain magnetic resonances belonging to two freely available data-sets for research purposes. The results are encouraging: we obtain an accuracy of 99% for the benign grade I and the II, III and IV malignant brain cancer detection. CONCLUSION: The experimental results confirm that the ensemble learner designed with the proposed method outperforms the current state-of-the-art approaches in brain cancer grade detection starting from magnetic resonance images.

Formal methods for prostate cancer gleason score and treatment prediction using radiomic biomarkers

  • Brunese, Luca
  • Mercaldo, Francesco
  • Reginelli, Alfonso
  • Santone, Antonella
Magnetic resonance imaging 2020 Journal Article, cited 11 times
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Quantitative variations in texture analysis features dependent on MRI scanning parameters: A phantom model

  • Buch, Karen
  • Kuno, Hirofumi
  • Qureshi, Muhammad M
  • Li, Baojun
  • Sakai, Osamu
Journal of applied clinical medical physics 2018 Journal Article, cited 0 times
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Quantitative Imaging Biomarker Ontology (QIBO) for Knowledge Representation of Biomedical Imaging Biomarkers

  • Buckler, AndrewJ
  • Ouellette, M.
  • Danagoulian, J.
  • Wernsing, G.
  • Liu, TiffanyTing
  • Savig, Erica
  • Suzek, BarisE
  • Rubin, DanielL
  • Paik, David
2013 Journal Article, cited 17 times
Website

Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm

  • Buda, Mateusz
  • Saha, Ashirbani
  • Mazurowski, Maciej A
2019 Journal Article, cited 1 times
Website
Recent analysis identified distinct genomic subtypes of lower-grade glioma tumors which are associated with shape features. In this study, we propose a fully automatic way to quantify tumor imaging characteristics using deep learning-based segmentation and test whether these characteristics are predictive of tumor genomic subtypes. We used preoperative imaging and genomic data of 110 patients from 5 institutions with lower-grade gliomas from The Cancer Genome Atlas. Based on automatic deep learning segmentations, we extracted three features which quantify two-dimensional and three-dimensional characteristics of the tumors. Genomic data for the analyzed cohort of patients consisted of previously identified genomic clusters based on IDH mutation and 1p/19q co-deletion, DNA methylation, gene expression, DNA copy number, and microRNA expression. To analyze the relationship between the imaging features and genomic clusters, we conducted the Fisher exact test for 10 hypotheses for each pair of imaging feature and genomic subtype. To account for multiple hypothesis testing, we applied a Bonferroni correction. P-values lower than 0.005 were considered statistically significant. We found the strongest association between RNASeq clusters and the bounding ellipsoid volume ratio (p < 0.0002) and between RNASeq clusters and margin fluctuation (p < 0.005). In addition, we identified associations between bounding ellipsoid volume ratio and all tested molecular subtypes (p < 0.02) as well as between angular standard deviation and RNASeq cluster (p < 0.02). In terms of automatic tumor segmentation that was used to generate the quantitative image characteristics, our deep learning algorithm achieved a mean Dice coefficient of 82% which is comparable to human performance.

Comparing nonrigid registration techniques for motion corrected MR prostate diffusion imaging

  • Buerger, C
  • Sénégas, J
  • Kabus, S
  • Carolus, H
  • Schulz, H
  • Agarwal, H
  • Turkbey, B
  • Choyke, PL
  • Renisch, S
Medical Physics 2015 Journal Article, cited 4 times
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PURPOSE: T2-weighted magnetic resonance imaging (MRI) is commonly used for anatomical visualization in the pelvis area, such as the prostate, with high soft-tissue contrast. MRI can also provide functional information such as diffusion-weighted imaging (DWI) which depicts the molecular diffusion processes in biological tissues. The combination of anatomical and functional imaging techniques is widely used in oncology, e.g., for prostate cancer diagnosis and staging. However, acquisition-specific distortions as well as physiological motion lead to misalignments between T2 and DWI and consequently to a reduced diagnostic value. Image registration algorithms are commonly employed to correct for such misalignment. METHODS: The authors compare the performance of five state-of-the-art nonrigid image registration techniques for accurate image fusion of DWI with T2. RESULTS: Image data of 20 prostate patients with cancerous lesions or cysts were acquired. All registration algorithms were validated using intensity-based as well as landmark-based techniques. CONCLUSIONS: The authors' results show that the "fast elastic image registration" provides most accurate results with a target registration error of 1.07 +/- 0.41 mm at minimum execution times of 11 +/- 1 s.

Using computer‐extracted image phenotypes from tumors on breast magnetic resonance imaging to predict breast cancer pathologic stage

  • Burnside, Elizabeth S
  • Drukker, Karen
  • Li, Hui
  • Bonaccio, Ermelinda
  • Zuley, Margarita
  • Ganott, Marie
  • Net, Jose M
  • Sutton, Elizabeth J
  • Brandt, Kathleen R
  • Whitman, Gary J
Cancer 2016 Journal Article, cited 28 times
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Selective segmentation of a feature that has two distinct intensities

  • Burrows, Liam
  • Chen, Ke
  • Torella, Francesco
Journal of Algorithms & Computational Technology 2021 Journal Article, cited 0 times
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It is common for a segmentation model to compute and locate edges or regions separated by edges according to a certain distribution of intensity. However such edge information is not always useful to extract an object or feature that has two distinct intensities e.g. segmentation of a building with signages in front or of an organ that has diseased regions, unless some of kind of manual editing is applied or a learning idea is used. This paper proposes an automatic and selective segmentation model that can segment a feature that has two distinct intensities by a single click. A patch like idea is employed to design our two stage model, given only one geometric marker to indicate the location of the inside region. The difficult case where the inside region is leaning towards the boundary of the interested feature is investigated with recommendations given and reliability tested. The model is mainly presented 2D but it can be easily generalised to 3D. We have implemented the model for segmenting both 2D and 3D images.

Medical Image Retrieval Based on Convolutional Neural Network and Supervised Hashing

  • Cai, Yiheng
  • Li, Yuanyuan
  • Qiu, Changyan
  • Ma, Jie
  • Gao, Xurong
IEEE Access 2019 Journal Article, cited 0 times
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In recent years, with extensive application in image retrieval and other tasks, a convolutional neural network (CNN) has achieved outstanding performance. In this paper, a new content-based medical image retrieval (CBMIR) framework using CNN and hash coding is proposed. The new framework adopts a Siamese network in which pairs of images are used as inputs, and a model is learned to make images belonging to the same class have similar features by using weight sharing and a contrastive loss function. In each branch of the network, CNN is adapted to extract features, followed by hash mapping, which is used to reduce the dimensionality of feature vectors. In the training process, a new loss function is designed to make the feature vectors more distinguishable, and a regularization term is added to encourage the real value outputs to approximate the desired binary values. In the retrieval phase, the compact binary hash code of the query image is achieved from the trained network and is subsequently compared with the hash codes of the database images. We experimented on two medical image datasets: the cancer imaging archive-computed tomography (TCIA-CT) and the vision and image analysis group/international early lung cancer action program (VIA/I-ELCAP). The results indicate that our method is superior to existing hash methods and CNN methods. Compared with the traditional hashing method, feature extraction based on CNN has advantages. The proposed algorithm combining a Siamese network with the hash method is superior to the classical CNN-based methods. The application of a new loss function can effectively improve retrieval accuracy.

A quantitative model based on clinically relevant MRI features differentiates lower grade gliomas and glioblastoma

  • Cao, H.
  • Erson-Omay, E. Z.
  • Li, X.
  • Gunel, M.
  • Moliterno, J.
  • Fulbright, R. K.
Eur Radiol 2020 Journal Article, cited 0 times
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OBJECTIVES: To establish a quantitative MR model that uses clinically relevant features of tumor location and tumor volume to differentiate lower grade glioma (LRGG, grades II and III) and glioblastoma (GBM, grade IV). METHODS: We extracted tumor location and tumor volume (enhancing tumor, non-enhancing tumor, peritumor edema) features from 229 The Cancer Genome Atlas (TCGA)-LGG and TCGA-GBM cases. Through two sampling strategies, i.e., institution-based sampling and repeat random sampling (10 times, 70% training set vs 30% validation set), LASSO (least absolute shrinkage and selection operator) regression and nine-machine learning method-based models were established and evaluated. RESULTS: Principal component analysis of 229 TCGA-LGG and TCGA-GBM cases suggested that the LRGG and GBM cases could be differentiated by extracted features. For nine machine learning methods, stack modeling and support vector machine achieved the highest performance (institution-based sampling validation set, AUC > 0.900, classifier accuracy > 0.790; repeat random sampling, average validation set AUC > 0.930, classifier accuracy > 0.850). For the LASSO method, regression model based on tumor frontal lobe percentage and enhancing and non-enhancing tumor volume achieved the highest performance (institution-based sampling validation set, AUC 0.909, classifier accuracy 0.830). The formula for the best performance of the LASSO model was established. CONCLUSIONS: Computer-generated, clinically meaningful MRI features of tumor location and component volumes resulted in models with high performance (validation set AUC > 0.900, classifier accuracy > 0.790) to differentiate lower grade glioma and glioblastoma. KEY POINTS: * Lower grade glioma and glioblastoma have significant different location and component volume distributions. * We built machine learning prediction models that could help accurately differentiate lower grade gliomas and GBM cases. We introduced a fast evaluation model for possible clinical differentiation and further analysis.

FPB: Improving Multi-Scale Feature Representation Inside Convolutional Layer Via Feature Pyramid Block

  • Cao, Zheng
  • Zhang, Kailai
  • Wu, Ji
2020 Conference Paper, cited 0 times
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Multi-scale features exist widely in biomedical images. For example, the scale of lesions may vary greatly according to different diseases. Effective representation of multi-scale features is essential for fully perceiving and understanding objects, which guarantees the performance of models. However, in biomedical image tasks, the insufficiency of data may prevent models from effectively capturing multi-scale features. In this paper, we propose Feature Pyramid Block (FPB), a novel structure to improve multi-scale feature representation within a single convolutional layer, which can be easily plugged into existing convolutional networks. Experiments on public biomedical image datasets prove consistent performance improvement with FPB. Furthermore, the convergence speed is faster and the computational costs are lower when using FPB, which proves high efficiency of our method.

Head and neck cancer patient images for determining auto-segmentation accuracy in T2-weighted magnetic resonance imaging through expert manual segmentations

  • Cardenas, Carlos E
  • Mohamed, Abdallah S R
  • Yang, Jinzhong
  • Gooding, Mark
  • Veeraraghavan, Harini
  • Kalpathy-Cramer, Jayashree
  • Ng, Sweet Ping
  • Ding, Yao
  • Wang, Jihong
  • Lai, Stephen Y
  • Fuller, Clifton D
  • Sharp, Greg
Med Phys 2020 Dataset, cited 0 times
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PURPOSE: The use of magnetic resonance imaging (MRI) in radiotherapy treatment planning has rapidly increased due to its ability to evaluate patient's anatomy without the use of ionizing radiation and due to its high soft tissue contrast. For these reasons, MRI has become the modality of choice for longitudinal and adaptive treatment studies. Automatic segmentation could offer many benefits for these studies. In this work, we describe a T2-weighted MRI dataset of head and neck cancer patients that can be used to evaluate the accuracy of head and neck normal tissue auto-segmentation systems through comparisons to available expert manual segmentations. ACQUISITION AND VALIDATION METHODS: T2-weighted MRI images were acquired for 55 head and neck cancer patients. These scans were collected after radiotherapy computed tomography (CT) simulation scans using a thermoplastic mask to replicate patient treatment position. All scans were acquired on a single 1.5 T Siemens MAGNETOM Aera MRI with two large four-channel flex phased-array coils. The scans covered the region encompassing the nasopharynx region cranially and supraclavicular lymph node region caudally, when possible, in the superior-inferior direction. Manual contours were created for the left/right submandibular gland, left/right parotids, left/right lymph node level II, and left/right lymph node level III. These contours underwent quality assurance to ensure adherence to predefined guidelines, and were corrected if edits were necessary. DATA FORMAT AND USAGE NOTES: The T2-weighted images and RTSTRUCT files are available in DICOM format. The regions of interest are named based on AAPM's Task Group 263 nomenclature recommendations (Glnd_Submand_L, Glnd_Submand_R, LN_Neck_II_L, Parotid_L, Parotid_R, LN_Neck_II_R, LN_Neck_III_L, LN_Neck_III_R). This dataset is available on The Cancer Imaging Archive (TCIA) by the National Cancer Institute under the collection "AAPM RT-MAC Grand Challenge 2019" (https://doi.org/10.7937/tcia.2019.bcfjqfqb). POTENTIAL APPLICATIONS: This dataset provides head and neck patient MRI scans to evaluate auto-segmentation systems on T2-weighted images. Additional anatomies could be provided at a later time to enhance the existing library of contours.

Standardization of brain MR images across machines and protocols: bridging the gap for MRI-based radiomics

  • Carré, Alexandre
  • Klausner, Guillaume
  • Edjlali, Myriam
  • Lerousseau, Marvin
  • Briend-Diop, Jade
  • Sun, Roger
  • Ammari, Samy
  • Reuzé, Sylvain
  • Andres, Emilie Alvarez
  • Estienne, Théo
Sci RepScientific reports 2020 Journal Article, cited 0 times
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PARaDIM - A PHITS-based Monte Carlo tool for internal dosimetry with tetrahedral mesh computational phantoms

  • Carter, L. M.
  • Crawford, T. M.
  • Sato, T.
  • Furuta, T.
  • Choi, C.
  • Kim, C. H.
  • Brown, J. L.
  • Bolch, W. E.
  • Zanzonico, P. B.
  • Lewis, J. S.
J Nucl Med 2019 Journal Article, cited 0 times
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Mesh-type and voxel-based computational phantoms comprise the current state-of-the-art for internal dose assessment via Monte Carlo simulations, but excel in different aspects, with mesh-type phantoms offering advantages over their voxel counterparts in terms of their flexibility and realistic representation of detailed patient- or subject-specific anatomy. We have developed PARaDIM, a freeware application for implementing tetrahedral mesh-type phantoms in absorbed dose calculations via the Particle and Heavy Ion Transport code System (PHITS). It considers all medically relevant radionuclides including alpha, beta, gamma, positron, and Auger/conversion electron emitters, and handles calculation of mean dose to individual regions, as well as 3D dose distributions for visualization and analysis in a variety of medical imaging softwares. This work describes the development of PARaDIM, documents the measures taken to test and validate its performance, and presents examples to illustrate its uses. Methods: Human, small animal, and cell-level dose calculations were performed with PARaDIM and the results compared with those of widely accepted dosimetry programs and literature data. Several tetrahedral phantoms were developed or adapted using computer-aided modeling techniques for these comparisons. Results: For human dose calculations, agreement of PARaDIM with OLINDA 2.0 was good - within 10-20% for most organs - despite geometric differences among the phantoms tested. Agreement with MIRDcell for cell-level S-value calculations was within 5% in most cases. Conclusion: PARaDIM extends the use of Monte Carlo dose calculations to the broader community in nuclear medicine by providing a user-friendly graphical user interface for calculation setup and execution. PARaDIM leverages the enhanced anatomical realism provided by advanced computational reference phantoms or bespoke image-derived phantoms to enable improved assessments of radiation doses in a variety of radiopharmaceutical use cases, research, and preclinical development.

Multimodal mixed reality visualisation for intraoperative surgical guidance

  • Cartucho, João
  • Shapira, David
  • Ashrafian, Hutan
  • Giannarou, Stamatia
International Journal of Computer Assisted Radiology and Surgery 2020 Journal Article, cited 0 times
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Development and external validation of a non-invasive molecular status predictor of chromosome 1p/19q co-deletion based on MRI radiomics analysis of Low Grade Glioma patients

  • Casale, R.
  • Lavrova, E.
  • Sanduleanu, S.
  • Woodruff, H. C.
  • Lambin, P.
Eur J Radiol 2021 Journal Article, cited 0 times
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PURPOSE: The 1p/19q co-deletion status has been demonstrated to be a prognostic biomarker in lower grade glioma (LGG). The objective of this study was to build a magnetic resonance (MRI)-derived radiomics model to predict the 1p/19q co-deletion status. METHOD: 209 pathology-confirmed LGG patients from 2 different datasets from The Cancer Imaging Archive were retrospectively reviewed; one dataset with 159 patients as the training and discovery dataset and the other one with 50 patients as validation dataset. Radiomics features were extracted from T2- and T1-weighted post-contrast MRI resampled data using linear and cubic interpolation methods. For each of the voxel resampling methods a three-step approach was used for feature selection and a random forest (RF) classifier was trained on the training dataset. Model performance was evaluated on training and validation datasets and clinical utility indexes (CUIs) were computed. The distributions and intercorrelation for selected features were analyzed. RESULTS: Seven radiomics features were selected from the cubic interpolated features and five from the linear interpolated features on the training dataset. The RF classifier showed similar performance for cubic and linear interpolation methods in the training dataset with accuracies of 0.81 (0.75-0.86) and 0.76 (0.71-0.82) respectively; in the validation dataset the accuracy dropped to 0.72 (0.6-0.82) using cubic interpolation and 0.72 (0.6-0.84) using linear resampling. CUIs showed the model achieved satisfactory negative values (0.605 using cubic interpolation and 0.569 for linear interpolation). CONCLUSIONS: MRI has the potential for predicting the 1p/19q status in LGGs. Both cubic and linear interpolation methods showed similar performance in external validation.

The Impact of Normalization Approaches to Automatically Detect Radiogenomic Phenotypes Characterizing Breast Cancer Receptors Status

  • Castaldo, Rossana
  • Pane, Katia
  • Nicolai, Emanuele
  • Salvatore, Marco
  • Franzese, Monica
Cancers (Basel) 2020 Journal Article, cited 0 times
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In breast cancer studies, combining quantitative radiomic with genomic signatures can help identifying and characterizing radiogenomic phenotypes, in function of molecular receptor status. Biomedical imaging processing lacks standards in radiomic feature normalization methods and neglecting feature normalization can highly bias the overall analysis. This study evaluates the effect of several normalization techniques to predict four clinical phenotypes such as estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and triple negative (TN) status, by quantitative features. The Cancer Imaging Archive (TCIA) radiomic features from 91 T1-weighted Dynamic Contrast Enhancement MRI of invasive breast cancers were investigated in association with breast invasive carcinoma miRNA expression profiling from the Cancer Genome Atlas (TCGA). Three advanced machine learning techniques (Support Vector Machine, Random Forest, and Naive Bayesian) were investigated to distinguish between molecular prognostic indicators and achieved an area under the ROC curve (AUC) values of 86%, 93%, 91%, and 91% for the prediction of ER+ versus ER-, PR+ versus PR-, HER2+ versus HER2-, and triple-negative, respectively. In conclusion, radiomic features enable to discriminate major breast cancer molecular subtypes and may yield a potential imaging biomarker for advancing precision medicine.

Selección de un algoritmo para la clasificación de Nódulos Pulmonares Solitarios

  • Castro, Arelys Rivero
  • Correa, Luis Manuel Cruz
  • Lezcano, Jeffrey Artiles
Revista Cubana de Informática Médica 2016 Journal Article, cited 0 times
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MRI volume changes of axillary lymph nodes as predictor of pathological complete responses to neoadjuvant chemotherapy in breast cancer

  • Cattell, Renee F.
  • Kang, James J.
  • Ren, Thomas
  • Huang, Pauline B.
  • Muttreja, Ashima
  • Dacosta, Sarah
  • Li, Haifang
  • Baer, Lea
  • Clouston, Sean
  • Palermo, Roxanne
  • Fisher, Paul
  • Bernstein, Cliff
  • Cohen, Jules A.
  • Duong, Tim Q.
Clinical Breast Cancer 2019 Journal Article, cited 0 times
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Introduction Longitudinal monitoring of breast tumor volume over the course of chemotherapy is informative of pathological response. This study aims to determine whether axillary lymph node (aLN) volume by MRI could augment the prediction accuracy of treatment response to neoadjuvant chemotherapy (NAC). Materials and Methods Level-2a curated data from I-SPY-1 TRIAL (2002-2006) were used. Patients had stage 2 or 3 breast cancer. MRI was acquired pre-, during and post-NAC. A subset with visible aLN on MRI was identified (N=132). Prediction of pathological complete response (PCR) was made using breast tumor volume changes, nodal volume changes, and combined breast tumor and nodal volume changes with sub-stratification with and without large lymph nodes (3mL or ∼1.79cm diameter cutoff). Receiver-operator-curve analysis was used to quantify prediction performance. Results Rate of change of aLN and breast tumor volume were informative of pathological response, with prediction being most informative early in treatment (AUC: 0.63-0.82) compared to later in treatment (AUC: 0.50-0.73). Larger aLN volume was associated with hormone receptor negativity, with the largest nodal volume for triple negative subtypes. Sub-stratification by node size improved predictive performance, with the best predictive model for large nodes having AUC of 0.82. Conclusion Axillary lymph node MRI offers clinically relevant information and has the potential to predict treatment response to neoadjuvant chemotherapy in breast cancer patients.

Highly accurate model for prediction of lung nodule malignancy with CT scans

  • Causey, Jason L
  • Zhang, Junyu
  • Ma, Shiqian
  • Jiang, Bo
  • Qualls, Jake A
  • Politte, David G
  • Prior, Fred
  • Zhang, Shuzhong
  • Huang, Xiuzhen
Sci RepScientific reports 2018 Journal Article, cited 5 times
Website
Computed tomography (CT) examinations are commonly used to predict lung nodule malignancy in patients, which are shown to improve noninvasive early diagnosis of lung cancer. It remains challenging for computational approaches to achieve performance comparable to experienced radiologists. Here we present NoduleX, a systematic approach to predict lung nodule malignancy from CT data, based on deep learning convolutional neural networks (CNN). For training and validation, we analyze >1000 lung nodules in images from the LIDC/IDRI cohort. All nodules were identified and classified by four experienced thoracic radiologists who participated in the LIDC project. NoduleX achieves high accuracy for nodule malignancy classification, with an AUC of ~0.99. This is commensurate with the analysis of the dataset by experienced radiologists. Our approach, NoduleX, provides an effective framework for highly accurate nodule malignancy prediction with the model trained on a large patient population. Our results are replicable with software available at http://bioinformatics.astate.edu/NoduleX .

Detection of Tumor Slice in Brain Magnetic Resonance Images by Feature Optimized Transfer Learning

  • Celik, Salih
  • KASIM, Ömer
Aksaray University Journal of Science and Engineering 2020 Journal Article, cited 0 times
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Renal cell carcinoma: predicting RUNX3 methylation level and its consequences on survival with CT features

  • Dongzhi Cen
  • Li Xu
  • Siwei Zhang
  • Zhiguang Chen
  • Yan Huang
  • Ziqi Li
  • Bo Liang
European Radiology 2019 Journal Article, cited 0 times
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PURPOSE: To investigate associations between CT imaging features, RUNX3 methylation level, and survival in clear cell renal cell carcinoma (ccRCC). MATERIALS AND METHODS: Patients were divided into high RUNX3 methylation and low RUNX3 methylation groups according to RUNX3 methylation levels (the threshold was identified by using X-tile). The CT scanning data from 106 ccRCC patients were retrospectively analyzed. The relationship between RUNX3 methylation level and overall survivals was evaluated using the Kaplan-Meyer analysis and Cox regression analysis (univariate and multivariate). The relationship between RUNX3 methylation level and CT features was evaluated using chi-square test and logistic regression analysis (univariate and multivariate). RESULTS: beta value cutoff of 0.53 to distinguish high methylation (N = 44) from low methylation tumors (N = 62). Patients with lower levels of methylation had longer median overall survival (49.3 vs. 28.4) months (low vs. high, adjusted hazard ratio [HR] 4.933, 95% CI 2.054-11.852, p < 0.001). On univariate logistic regression analysis, four risk factors (margin, side, long diameter, and intratumoral vascularity) were associated with RUNX3 methylation level (all p < 0.05). Multivariate logistic regression analysis found that three risk factors (side: left vs. right, odds ratio [OR] 2.696; p = 0.024; 95% CI 1.138-6.386; margin: ill-defined vs. well-defined, OR 2.685; p = 0.038; 95% CI 1.057-6.820; and intratumoral vascularity: yes vs. no, OR 3.286; p = 0.008; 95% CI 1.367-7.898) were significant independent predictors of high methylation tumors. This model had an area under the receiver operating characteristic curve (AUC) of 0.725 (95% CI 0.623-0.827). CONCLUSIONS: Higher levels of RUNX3 methylation are associated with shorter survival in ccRCC patients. And presence of intratumoral vascularity, ill-defined margin, and left side tumor were significant independent predictors of high methylation level of RUNX3 gene. KEY POINTS: * RUNX3 methylation level is negatively associated with overall survival in ccRCC patients. * Presence of intratumoral vascularity, ill-defined margin, and left side tumor were significant independent predictors of high methylation level of RUNX3 gene.

Segmentation, tracking, and kinematics of lung parenchyma and lung tumors from 4D CT with application to radiation treatment planning

  • Cha, Jungwon
2018 Thesis, cited 0 times
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This thesis is concerned with development of techniques for efficient computerized analysis of 4-D CT data. The goal is to have a highly automated approach to segmentation of the lung boundary and lung nodules inside the lung. The determination of exact lung tumor location over space and time by image segmentation is an essential step to track thoracic malignancies. Accurate image segmentation helps clinical experts examine the anatomy and structure and determine the disease progress. Since 4-D CT provides structural and anatomical information during tidal breathing, we use the same data to also measure mechanical properties related to deformation of the lung tissue including Jacobian and strain at high resolutions and as a function of time. Radiation Treatment of patients with lung cancer can benefit from knowledge of these measures of regional ventilation. Graph-cuts techniques have been popular for image segmentation since they are able to treat highly textured data via robust global optimization, avoiding local minima in graph based optimization. The graph-cuts methods have been used to extract globally optimal boundaries from images by s/t cut, with energy function based on model-specific visual cues, and useful topological constraints. The method makes N-dimensional globally optimal segmentation possible with good computational efficiency. Even though the graph-cuts method can extract objects where there is a clear intensity difference, segmentation of organs or tumors pose a challenge. For organ segmentation, many segmentation methods using a shape prior have been proposed. However, in the case of lung tumors, the shape varies from patient to patient, and with location. In this thesis, we use a shape prior for tumors through a training step and PCA analysis based on the Active Shape Model (ASM). The method has been tested on real patient data from the Brown Cancer Center at the University of Louisville. We performed temporal B-spline deformable registration of the 4-D CT data - this yielded 3-D deformation fields between successive respiratory phases from which measures of regional lung function were determined. During the respiratory cycle, the lung volume changes and five different lobes of the lung (two in the left and three in the right lung) show different deformation yielding different strain and Jacobian maps. In this thesis, we determine the regional lung mechanics in the Lagrangian frame of reference through different respiratory phases, for example, Phase10 to 20, Phase10 to 30, Phase10 to 40, and Phase10 to 50. Single photon emission computed tomography (SPECT) lung imaging using radioactive tracers with SPECT ventilation and SPECT perfusion imaging also provides functional information. As part of an IRB-approved study therefore, we registered the max-inhale CT volume to both VSPECT and QSPECT data sets using the Demon's non-rigid registration algorithm in patient subjects. Subsequently, statistical correlation between CT ventilation images (Jacobian and strain values), with both VSPECT and QSPECT was undertaken. Through statistical analysis with the Spearman's rank correlation coefficient, we found that Jacobian values have the highest correlation with both VSPECT and QSPECT.

Segmentation and tracking of lung nodules via graph‐cuts incorporating shape prior and motion from 4D CT

  • Cha, Jungwon
  • Farhangi, Mohammad Mehdi
  • Dunlap, Neal
  • Amini, Amir A
Medical Physics 2018 Journal Article, cited 5 times
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Evaluation of data augmentation via synthetic images for improved breast mass detection on mammograms using deep learning

  • Cha, K. H.
  • Petrick, N.
  • Pezeshk, A.
  • Graff, C. G.
  • Sharma, D.
  • Badal, A.
  • Sahiner, B.
J Med Imaging (Bellingham) 2020 Journal Article, cited 1 times
Website
We evaluated whether using synthetic mammograms for training data augmentation may reduce the effects of overfitting and increase the performance of a deep learning algorithm for breast mass detection. Synthetic mammograms were generated using in silico procedural analytic breast and breast mass modeling algorithms followed by simulated x-ray projections of the breast models into mammographic images. In silico breast phantoms containing masses were modeled across the four BI-RADS breast density categories, and the masses were modeled with different sizes, shapes, and margins. A Monte Carlo-based x-ray transport simulation code, MC-GPU, was used to project the three-dimensional phantoms into realistic synthetic mammograms. 2000 mammograms with 2522 masses were generated to augment a real data set during training. From the Curated Breast Imaging Subset of the Digital Database for Screening Mammography (CBIS-DDSM) data set, we used 1111 mammograms (1198 masses) for training, 120 mammograms (120 masses) for validation, and 361 mammograms (378 masses) for testing. We used faster R-CNN for our deep learning network with pretraining from ImageNet using the Resnet-101 architecture. We compared the detection performance when the network was trained using different percentages of the real CBIS-DDSM training set (100%, 50%, and 25%), and when these subsets of the training set were augmented with 250, 500, 1000, and 2000 synthetic mammograms. Free-response receiver operating characteristic (FROC) analysis was performed to compare performance with and without the synthetic mammograms. We generally observed an improved test FROC curve when training with the synthetic images compared to training without them, and the amount of improvement depended on the number of real and synthetic images used in training. Our study shows that enlarging the training data with synthetic samples can increase the performance of deep learning systems.

Computational assessment of stomach tumor volume from multi-slice computerized tomography images in presence of type 2 cancer

  • Chacón, Gerardo
  • Rodríguez, Johel E
  • Bermúdez, Valmore
  • Vera, Miguel
  • Hernández, Juan Diego
  • Vargas, Sandra
  • Pardo, Aldo
  • Lameda, Carlos
  • Madriz, Delia
  • Bravo, Antonio J
F1000Research 2018 Journal Article, cited 0 times
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Background: The multi-slice computerized tomography (MSCT) is a medical imaging modality that has been used to determine the size and location of the stomach cancer. Additionally, MSCT is considered the best modality for the staging of gastric cancer. One way to assess the type 2 cancer of stomach is by detecting the pathological structure with an image segmentation approach. The tumor segmentation of MSCT gastric cancer images enables the diagnosis of the disease condition, for a given patient, without using an invasive method as surgical intervention. Methods: This approach consists of three stages. The initial stage, an image enhancement, consists of a method for correcting non homogeneities present in the background of MSCT images. Then, a segmentation stage using a clustering method allows to obtain the adenocarcinoma morphology. In the third stage, the pathology region is reconstructed and then visualized with a three-dimensional (3-D) computer graphics procedure based on marching cubes algorithm. In order to validate the segmentations, the Dice score is used as a metric function useful for comparing the segmentations obtained using the proposed method with respect to ground truth volumes traced by a clinician. Results: A total of 8 datasets available for patients diagnosed, from the cancer data collection of the project, Cancer Genome Atlas Stomach Adenocarcinoma (TCGASTAD) is considered in this research. The volume of the type 2 stomach tumor is estimated from the 3-D shape computationally segmented from the each dataset. These 3-D shapes are computationally reconstructed and then used to assess the morphopathology macroscopic features of this cancer. Conclusions: The segmentations obtained are useful for assessing qualitatively and quantitatively the stomach type 2 cancer. In addition, this type of segmentation allows the development of computational models that allow the planning of virtual surgical processes related to type 2 cancer.

Automated feature extraction in brain tumor by magnetic resonance imaging using gaussian mixture models

  • Chaddad, Ahmad
Journal of Biomedical Imaging 2015 Journal Article, cited 29 times
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GBM heterogeneity characterization by radiomic analysis of phenotype anatomical planes

  • Chaddad, Ahmad
  • Desrosiers, Christian
  • Toews, Matthew
2016 Conference Proceedings, cited 4 times
Website

Radiomic analysis of multi-contrast brain MRI for the prediction of survival in patients with glioblastoma multiforme

  • Chaddad, Ahmad
  • Desrosiers, Christian
  • Toews, Matthew
2016 Conference Proceedings, cited 11 times
Website
Image texture features are effective at characterizing the microstructure of cancerous tissues. This paper proposes predicting the survival times of glioblastoma multiforme (GBM) patients using texture features extracted in multi-contrast brain MRI images. Texture features are derived locally from contrast enhancement, necrosis and edema regions in T1-weighted post-contrast and fluid-attenuated inversion-recovery (FLAIR) MRIs, based on the gray-level co-occurrence matrix representation. A statistical analysis based on the Kaplan-Meier method and log-rank test is used to identify the texture features related with the overall survival of GBM patients. Results are presented on a dataset of 39 GBM patients. For FLAIR images, four features (Energy, Correlation, Variance and Inverse of Variance) from contrast enhancement regions and a feature (Homogeneity) from edema regions were shown to be associated with survival times (p-value <; 0.01). Likewise, in T1-weighted images, three features (Energy, Correlation, and Variance) from contrast enhancement regions were found to be useful for predicting the overall survival of GBM patients. These preliminary results show the advantages of texture analysis in predicting the prognosis of GBM patients from multi-contrast brain MRI.

Phenotypic characterization of glioblastoma identified through shape descriptors

  • Chaddad, Ahmad
  • Desrosiers, Christian
  • Toews, Matthew
2016 Conference Proceedings, cited 4 times
Website
This paper proposes quantitatively describing the shape of glioblastoma (GBM) tissue phenotypes as a set of shape features derived from segmentations, for the purposes of discriminating between GBM phenotypes and monitoring tumor progression. GBM patients were identified from the Cancer Genome Atlas, and quantitative MR imaging data were obtained from the Cancer Imaging Archive. Three GBM tissue phenotypes are considered including necrosis, active tumor and edema/invasion. Volumetric tissue segmentations are obtained from registered T1˗weighted (T1˗WI) postcontrast and fluid-attenuated inversion recovery (FLAIR) MRI modalities. Shape features are computed from respective tissue phenotype segmentations, and a Kruskal-Wallis test was employed to select features capable of classification with a significance level of p < 0.05. Several classifier models are employed to distinguish phenotypes, where a leave-one-out cross-validation was performed. Eight features were found statistically significant for classifying GBM phenotypes with p <0.05, orientation is uninformative. Quantitative evaluations show the SVM results in the highest classification accuracy of 87.50%, sensitivity of 94.59% and specificity of 92.77%. In summary, the shape descriptors proposed in this work show high performance in predicting GBM tissue phenotypes. They are thus closely linked to morphological characteristics of GBM phenotypes and could potentially be used in a computer assisted labeling system.

Predicting survival time of lung cancer patients using radiomic analysis

  • Chaddad, Ahmad
  • Desrosiers, Christian
  • Toews, Matthew
  • Abdulkarim, Bassam
OncotargetOncotarget 2017 Journal Article, cited 4 times
Website
Objectives: This study investigates the prediction of Non-small cell lung cancer (NSCLC) patient survival outcomes based on radiomic texture and shape features automatically extracted from tumor image data. Materials and Methods: Retrospective analysis involves CT scans of 315 NSCLC patients from The Cancer Imaging Archive (TCIA). A total of 24 image features are computed from labeled tumor volumes of patients within groups defined using NSCLC subtype and TNM staging information. Spearman's rank correlation, Kaplan-Meier estimation and log-rank tests were used to identify features related to long/short NSCLC patient survival groups. Automatic random forest classification was used to predict patient survival group from multivariate feature data. Significance is assessed at P < 0.05 following Holm-Bonferroni correction for multiple comparisons. Results: Significant correlations between radiomic features and survival were observed for four clinical groups: (group, [absolute correlation range]): (large cell carcinoma (LCC) [0.35, 0.43]), (tumor size T2, [0.31, 0.39]), (non lymph node metastasis N0, [0.3, 0.33]), (TNM stage I, [0.39, 0.48]). Significant log-rank relationships between features and survival time were observed for three clinical groups: (group, hazard ratio): (LCC, 3.0), (LCC, 3.9), (T2, 2.5) and (stage I, 2.9). Automatic survival prediction performance (i.e. below/above median) is superior for combined radiomic features with age-TNM in comparison to standard TNM clinical staging information (clinical group, mean area-under-the-ROC-curve (AUC)): (LCC, 75.73%), (N0, 70.33%), (T2, 70.28%) and (TNM-I, 76.17%). Conclusion: Quantitative lung CT imaging features can be used as indicators of survival, in particular for patients with large-cell-carcinoma (LCC), primary-tumor-sizes (T2) and no lymph-node-metastasis (N0).

Multimodal Radiomic Features for the Predicting Gleason Score of Prostate Cancer

  • Chaddad, Ahmad
  • Kucharczyk, Michael
  • Niazi, Tamim
Cancers 2018 Journal Article, cited 1 times
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Predicting Gleason Score of Prostate Cancer Patients using Radiomic Analysis

  • Chaddad, Ahmad
  • Niazi, Tamim
  • Probst, Stephan
  • Bladou, Franck
  • Anidjar, Moris
  • Bahoric, Boris
Frontiers in Oncology 2018 Journal Article, cited 0 times
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Prediction of survival with multi-scale radiomic analysis in glioblastoma patients

  • Chaddad, Ahmad
  • Sabri, Siham
  • Niazi, Tamim
  • Abdulkarim, Bassam
2018 Journal Article, cited 1 times
Website
We propose a multiscale texture features based on Laplacian-of Gaussian (LoG) filter to predict progression free (PFS) and overall survival (OS) in patients newly diagnosed with glioblastoma (GBM). Experiments use the extracted features derived from 40 patients of GBM with T1-weighted imaging (T1-WI) and Fluid-attenuated inversion recovery (FLAIR) images that were segmented manually into areas of active tumor, necrosis, and edema. Multiscale texture features were extracted locally from each of these areas of interest using a LoG filter and the relation between features to OS and PFS was investigated using univariate (i.e., Spearman’s rank correlation coefficient, log-rank test and Kaplan-Meier estimator) and multivariate analyses (i.e., Random Forest classifier). Three and seven features were statistically correlated with PFS and OS, respectively, with absolute correlation values between 0.32 and 0.36 and p < 0.05. Three features derived from active tumor regions only were associated with OS (p < 0.05) with hazard ratios (HR) of 2.9, 3, and 3.24, respectively. Combined features showed an AUC value of 85.37 and 85.54% for predicting the PFS and OS of GBM patients, respectively, using the random forest (RF) classifier. We presented a multiscale texture features to characterize the GBM regions and predict the PFS and OS. The efficiency achievable suggests that this technique can be developed into a GBM MR analysis system suitable for clinical use after a thorough validation involving more patients.

High-Throughput Quantification of Phenotype Heterogeneity Using Statistical Features

  • Chaddad, Ahmad
  • Tanougast, Camel
Advances in Bioinformatics 2015 Journal Article, cited 5 times
Website
Statistical features are widely used in radiology for tumor heterogeneity assessment using magnetic resonance (MR) imaging technique. In this paper, feature selection based on decision tree is examined to determine the relevant subset of glioblastoma (GBM) phenotypes in the statistical domain. To discriminate between active tumor (vAT) and edema/invasion (vE) phenotype, we selected the significant features using analysis of variance (ANOVA) with p value < 0.01. Then, we implemented the decision tree to define the optimal subset features of phenotype classifier. Naive Bayes (NB), support vector machine (SVM), and decision tree (DT) classifier were considered to evaluate the performance of the feature based scheme in terms of its capability to discriminate vAT from vE. Whole nine features were statistically significant to classify the vAT from vE with p value < 0.01. Feature selection based on decision tree showed the best performance by the comparative study using full feature set. The feature selected showed that the two features Kurtosis and Skewness achieved a highest range value of 58.33-75.00% accuracy classifier and 73.88-92.50% AUC. This study demonstrated the ability of statistical features to provide a quantitative, individualized measurement of glioblastoma patient and assess the phenotype progression.

Quantitative evaluation of robust skull stripping and tumor detection applied to axial MR images

  • Chaddad, Ahmad
  • Tanougast, Camel
Brain Informatics 2016 Journal Article, cited 28 times
Website

Extracted magnetic resonance texture features discriminate between phenotypes and are associated with overall survival in glioblastoma multiforme patients

  • Chaddad, Ahmad
  • Tanougast, Camel
2016 Journal Article, cited 16 times
Website
GBM is a markedly heterogeneous brain tumor consisting of three main volumetric phenotypes identifiable on magnetic resonance imaging: necrosis (vN), active tumor (vAT), and edema/invasion (vE). The goal of this study is to identify the three glioblastoma multiforme (GBM) phenotypes using a texture-based gray-level co-occurrence matrix (GLCM) approach and determine whether the texture features of phenotypes are related to patient survival. MR imaging data in 40 GBM patients were analyzed. Phenotypes vN, vAT, and vE were segmented in a preprocessing step using 3D Slicer for rigid registration by T1-weighted imaging and corresponding fluid attenuation inversion recovery images. The GBM phenotypes were segmented using 3D Slicer tools. Texture features were extracted from GLCM of GBM phenotypes. Thereafter, Kruskal-Wallis test was employed to select the significant features. Robust predictive GBM features were identified and underwent numerous classifier analyses to distinguish phenotypes. Kaplan-Meier analysis was also performed to determine the relationship, if any, between phenotype texture features and survival rate. The simulation results showed that the 22 texture features were significant with p value < 0.05. GBM phenotype discrimination based on texture features showed the best accuracy, sensitivity, and specificity of 79.31, 91.67, and 98.75 %, respectively. Three texture features derived from active tumor parts: difference entropy, information measure of correlation, and inverse difference were statistically significant in the prediction of survival, with log-rank p values of 0.001, 0.001, and 0.008, respectively. Among 22 features examined, three texture features have the ability to predict overall survival for GBM patients demonstrating the utility of GLCM analyses in both the diagnosis and prognosis of this patient population.

Automated lung field segmentation in CT images using mean shift clustering and geometrical features

  • Chama, Chanukya Krishna
  • Mukhopadhyay, Sudipta
  • Biswas, Prabir Kumar
  • Dhara, Ashis Kumar
  • Madaiah, Mahendra Kasuvinahally
  • Khandelwal, Niranjan
2013 Conference Proceedings, cited 8 times
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Using Docker to support reproducible research

  • Chamberlain, Ryan
  • Invenshure, L
  • Schommer, Jennifer
2014 Report, cited 30 times
Website
Reproducible research is a growing movement among scientists, but the tools for creating sustainable software to support the computational side of research are still in their infancy and are typically only being used by scientists with expertise in computer programming and system administration. Docker is a new platform developed for the DevOps community that enables the easy creation and management of consistent computational environments. This article describes how we have applied it to computational science and suggests that it could be a powerful tool for reproducible research.

Automatic Classification of Brain Tumor Types with the MRI Scans and Histopathology Images

  • Chan, Hsiang-Wei
  • Weng, Yan-Ting
  • Huang, Teng-Yi
2020 Conference Paper, cited 0 times
Website
In the study, we used two neural networks, including VGG16 and Resnet50, to process the whole slide images with feature extracting. To classify the three types of brain tumors (i.e., glioblastoma, oligodendroglioma, and astrocytoma), we tried several clustering methods include k-means and random forest classification methods. In the prediction stage, we compared the prediction results with and without MRI features. The results support that the classification method performed with image features extracted by VGG16 has the highest prediction accuracy. Moreover, we found that combining with radiomics generated from MR images slightly improved the accuracy of the classification.

Residual Convolutional Neural Network for the Determination of IDH Status in Low-and High-Grade Gliomas from MR Imaging

  • Chang, Ken
  • Bai, Harrison X
  • Zhou, Hao
  • Su, Chang
  • Bi, Wenya Linda
  • Agbodza, Ena
  • Kavouridis, Vasileios K
  • Senders, Joeky T
  • Boaro, Alessandro
  • Beers, Andrew
Clinical Cancer Research 2018 Journal Article, cited 26 times
Website

Automatic assessment of glioma burden: A deep learning algorithm for fully automated volumetric and bi-dimensional measurement

  • Chang, Ken
  • Beers, Andrew L
  • Bai, Harrison X
  • Brown, James M
  • Ly, K Ina
  • Li, Xuejun
  • Senders, Joeky T
  • Kavouridis, Vasileios K
  • Boaro, Alessandro
  • Su, Chang
  • Bi, Wenya Linda
  • Rapalino, Otto
  • Liao, Weihua
  • Shen, Qin
  • Zhou, Hao
  • Xiao, Bo
  • Wang, Yinyan
  • Zhang, Paul J
  • Pinho, Marco C
  • Wen, Patrick Y
  • Batchelor, Tracy T
  • Boxerman, Jerrold L
  • Arnaout, Omar
  • Rosen, Bruce R
  • Gerstner, Elizabeth R
  • Yang, Li
  • Huang, Raymond Y
  • Kalpathy-Cramer, Jayashree
2019 Journal Article, cited 0 times
Website
BACKGROUND: Longitudinal measurement of glioma burden with MRI is the basis for treatment response assessment. In this study, we developed a deep learning algorithm that automatically segments abnormal FLAIR hyperintensity and contrast-enhancing tumor, quantitating tumor volumes as well as the product of maximum bi-dimensional diameters according to the Response Assessment in Neuro-Oncology (RANO) criteria (AutoRANO). METHODS: Two cohorts of patients were used for this study. One consisted of 843 pre-operative MRIs from 843 patients with low- or high-grade gliomas from four institutions and the second consisted 713 longitudinal, post-operative MRI visits from 54 patients with newly diagnosed glioblastomas (each with two pre-treatment "baseline" MRIs) from one institution. RESULTS: The automatically generated FLAIR hyperintensity volume, contrast-enhancing tumor volume, and AutoRANO were highly repeatable for the double-baseline visits, with an intraclass correlation coefficient (ICC) of 0.986, 0.991, and 0.977, respectivelyon the cohort of post-operative GBM patients. Furthermore, there was high agreement between manually and automatically measured tumor volumes, with ICC values of 0.915, 0.924, and 0.965 for pre-operative FLAIR hyperintensity, post-operative FLAIR hyperintensity, and post-operative contrast-enhancing tumor volumes, respectively. Lastly, the ICC for comparing manually and automatically derived longitudinal changes in tumor burden was 0.917, 0.966, and 0.850 for FLAIR hyperintensity volume, contrast-enhancing tumor volume, and RANO measures, respectively. CONCLUSIONS: Our automated algorithm demonstrates potential utility for evaluating tumor burden in complex post-treatment settings, although further validation in multi-center clinical trials will be needed prior to widespread implementation.

Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas

  • Chang, P
  • Grinband, J
  • Weinberg, BD
  • Bardis, M
  • Khy, M
  • Cadena, G
  • Su, M-Y
  • Cha, S
  • Filippi, CG
  • Bota, D
American Journal of Neuroradiology 2018 Journal Article, cited 5 times
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Primer for Image Informatics in Personalized Medicine

  • Chang, Young Hwan
  • Foley, Patrick
  • Azimi, Vahid
  • Borkar, Rohan
  • Lefman, Jonathan
Procedia Engineering 2016 Journal Article, cited 0 times
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A New General Maximum Intensity Projection Technology via the Hybrid of U-Net and Radial Basis Function Neural Network

  • Chao, Zhen
  • Xu, Wenting
2021 Journal Article, cited 0 times
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“Big data” and “open data”: What kind of access should researchers enjoy?

  • Chatellier, Gilles
  • Varlet, Vincent
  • Blachier-Poisson, Corinne
Thérapie 2016 Journal Article, cited 0 times

Investigating the impact of the CT Hounsfield unit range on radiomic feature stability using dual energy CT data

  • Chatterjee, A.
  • Vallieres, M.
  • Forghani, R.
  • Seuntjens, J.
Phys Med 2021 Journal Article, cited 0 times
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PURPOSE: Radiomic texture calculation requires discretizing image intensities within the region-of-interest. FBN (fixed-bin-number), FBS (fixed-bin-size) and FBN and FBS with intensity equalization (FBNequal, FBSequal) are four discretization approaches. A crucial choice is the voxel intensity (Hounsfield units, or HU) binning range. We assessed the effect of this choice on radiomic features. METHODS: The dataset comprised 95 patients with head-and-neck squamous-cell-carcinoma. Dual energy CT data was reconstructed at 21 electron energies (40, 45,... 140 keV). Each of 94 texture features were calculated with 64 extraction parameters. All features were calculated five times: original choice, left shift (-10/-20 HU), right shift (+10/+20 HU). For each feature, Spearman correlation between nominal and four variants were calculated to determine feature stability. This was done for six texture feature types (GLCM, GLRLM, GLSZM, GLDZM, NGTDM, and NGLDM) separately. This analysis was repeated for the four binning algorithms. Effect of feature instability on predictive ability was studied for lymphadenopathy as endpoint. RESULTS: FBN and FBNequal algorithms showed good stability (correlation values consistently >0.9). For FBS and FBSequal algorithms, while median values exceeded 0.9, the 95% lower bound decreased as a function of energy, with poor performance over the entire spectrum. FBNequal was the most stable algorithm, and FBS the least. CONCLUSIONS: We believe this is the first multi-energy systematic study of the impact of CT HU range used during intensity discretization for radiomic feature extraction. Future analyses should account for this source of uncertainty when evaluating the robustness of their radiomic signature.

MRI prostate cancer radiomics: Assessment of effectiveness and perspectives

  • Chatzoudis, Pavlos
2018 Thesis, cited 0 times
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A Fast Semi-Automatic Segmentation Tool for Processing Brain Tumor Images

  • Chen, Andrew X
  • Rabadán, Raúl
2017 Book Section, cited 0 times
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Low-dose CT via convolutional neural network

  • Chen, Hu
  • Zhang, Yi
  • Zhang, Weihua
  • Liao, Peixi
  • Li, Ke
  • Zhou, Jiliu
  • Wang, Ge
Biomedical Optics Express 2017 Journal Article, cited 342 times
Website
In order to reduce the potential radiation risk, low-dose CT has attracted an increasing attention. However, simply lowering the radiation dose will significantly degrade the image quality. In this paper, we propose a new noise reduction method for low-dose CT via deep learning without accessing original projection data. A deep convolutional neural network is here used to map low-dose CT images towards its corresponding normal-dose counterparts in a patch-by-patch fashion. Qualitative results demonstrate a great potential of the proposed method on artifact reduction and structure preservation. In terms of the quantitative metrics, the proposed method has showed a substantial improvement on PSNR, RMSE and SSIM than the competing state-of-art methods. Furthermore, the speed of our method is one order of magnitude faster than the iterative reconstruction and patch-based image denoising methods.

Generating anthropomorphic phantoms using fully unsupervised deformable image registration with convolutional neural networks

  • Chen, Junyu
  • Li, Ye
  • Du, Yong
  • Frey, Eric C
Med Phys 2020 Journal Article, cited 0 times
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PURPOSE: Computerized phantoms have been widely used in nuclear medicine imaging for imaging system optimization and validation. Although the existing computerized phantoms can model anatomical variations through organ and phantom scaling, they do not provide a way to fully reproduce the anatomical variations and details seen in humans. In this work, we present a novel registration-based method for creating highly anatomically detailed computerized phantoms. We experimentally show substantially improved image similarity of the generated phantom to a patient image. METHODS: We propose a deep-learning-based unsupervised registration method to generate a highly anatomically detailed computerized phantom by warping an XCAT phantom to a patient computed tomography (CT) scan. We implemented and evaluated the proposed method using the NURBS-based XCAT phantom and a publicly available low-dose CT dataset from TCIA. A rigorous tradeoff analysis between image similarity and deformation regularization was conducted to select the loss function and regularization term for the proposed method. A novel SSIM-based unsupervised objective function was proposed. Finally, ablation studies were conducted to evaluate the performance of the proposed method (using the optimal regularization and loss function) and the current state-of-the-art unsupervised registration methods. RESULTS: The proposed method outperformed the state-of-the-art registration methods, such as SyN and VoxelMorph, by more than 8%, measured by the SSIM and less than 30%, by the MSE. The phantom generated by the proposed method was highly detailed and was almost identical in appearance to a patient image. CONCLUSIONS: A deep-learning-based unsupervised registration method was developed to create anthropomorphic phantoms with anatomies labels that can be used as the basis for modeling organ properties. Experimental results demonstrate the effectiveness of the proposed method. The resulting anthropomorphic phantom is highly realistic. Combined with realistic simulations of the image formation process, the generated phantoms could serve in many applications of medical imaging research.

Aggregating Multi-scale Prediction Based on 3D U-Net in Brain Tumor Segmentation

  • Chen, Minglin
  • Wu, Yaozu
  • Wu, Jianhuang
2020 Conference Paper, cited 0 times
Website
Magnetic resonance imaging (MRI) is the dominant modality used in the initial evaluation of patients with primary brain tumors due to its superior image resolution and high safety profile. Automated segmentation of brain tumors from MRI is critical in the determination of response to therapy. In this paper, we propose a novel method which aggregates multi-scale prediction from 3D U-Net to segment enhancing tumor (ET), whole tumor (WT) and tumor core (TC) from multimodal MRI. Multi-scale prediction is derived from the decoder part of 3D U-Net at different resolutions. The final prediction takes the minimum value of the corresponding pixel from the upsampling multi-scale prediction. Aggregating multi-scale prediction can add constraints to the network which is beneficial for limited data. Additionally, we employ model ensembling strategy to further improve the performance of the proposed network. Finally, we achieve dice scores of 0.7745, 0.8640 and 0.7914, and Hausdorff distances (95th percentile) of 4.2365, 6.9381 and 6.6026 for ET, WT and TC respectively on the test set in BraTS 2019.

Radiomic Features at CT Can Distinguish Pancreatic Cancer from Noncancerous Pancreas

  • Chen, Po-Ting
  • Chang, Dawei
  • Yen, Huihsuan
  • Liu, Kao-Lang
  • Huang, Su-Yun
  • Roth, Holger
  • Wu, Ming-Shiang
  • Liao, Wei-Chih
  • Wang, Weichung
Radiol Imaging Cancer 2021 Journal Article, cited 0 times
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Purpose To identify distinguishing CT radiomic features of pancreatic ductal adenocarcinoma (PDAC) and to investigate whether radiomic analysis with machine learning can distinguish between patients who have PDAC and those who do not. Materials and Methods This retrospective study included contrast material-enhanced CT images in 436 patients with PDAC and 479 healthy controls from 2012 to 2018 from Taiwan that were randomly divided for training and testing. Another 100 patients with PDAC (enriched for small PDACs) and 100 controls from Taiwan were identified for testing (from 2004 to 2011). An additional 182 patients with PDAC and 82 healthy controls from the United States were randomly divided for training and testing. Images were processed into patches. An XGBoost (https://xgboost.ai/) model was trained to classify patches as cancerous or noncancerous. Patients were classified as either having or not having PDAC on the basis of the proportion of patches classified as cancerous. For both patch-based and patient-based classification, the models were characterized as either a local model (trained on Taiwanese data only) or a generalized model (trained on both Taiwanese and U.S. data). Sensitivity, specificity, and accuracy were calculated for patch- and patient-based analysis for the models. Results The median tumor size was 2.8 cm (interquartile range, 2.0-4.0 cm) in the 536 Taiwanese patients with PDAC (mean age, 65 years +/- 12 [standard deviation]; 289 men). Compared with normal pancreas, PDACs had lower values for radiomic features reflecting intensity and higher values for radiomic features reflecting heterogeneity. The performance metrics for the developed generalized model when tested on the Taiwanese and U.S. test data sets, respectively, were as follows: sensitivity, 94.7% (177 of 187) and 80.6% (29 of 36); specificity, 95.4% (187 of 196) and 100% (16 of 16); accuracy, 95.0% (364 of 383) and 86.5% (45 of 52); and area under the curve, 0.98 and 0.91. Conclusion Radiomic analysis with machine learning enabled accurate detection of PDAC at CT and could identify patients with PDAC. Keywords: CT, Computer Aided Diagnosis (CAD), Pancreas, Computer Applications-Detection/Diagnosis Supplemental material is available for this article. (c) RSNA, 2021.

A Joint Detection and Recognition Approach to Lung Cancer Diagnosis From CT Images With Label Uncertainty

  • Chenyang, L.
  • Chan, S. C.
IEEE Access 2020 Journal Article, cited 0 times
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Automatic lung cancer diagnosis from computer tomography (CT) images requires the detection of nodule location as well as nodule malignancy prediction. This article proposes a joint lung nodule detection and classification network for simultaneous lung nodule detection, segmentation and classification subject to possible label uncertainty in the training set. It operates in an end-to-end manner and provides detection and classification of nodules simultaneously together with a segmentation of the detected nodules. Both the nodule detection and classification subnetworks of the proposed joint network adopt a 3-D encoder-decoder architecture for better exploration of the 3-D data. Moreover, the classification subnetwork utilizes the features extracted from the detection subnetwork and multiscale nodule-specific features for boosting the classification performance. The former serves as valuable prior information for optimizing the more complicated 3D classification network directly to better distinguish suspicious nodules from other tissues compared with direct backpropagation from the decoder. Experimental results show that this co-training yields better performance on both tasks. The framework is validated on the LUNA16 and LIDC-IDRI datasets and a pseudo-label approach is proposed for addressing the label uncertainty problem due to inconsistent annotations/labels. Experimental results show that the proposed nodule detector outperforms the state-of-the-art algorithms and yields comparable performance as state-of-the-art nodule classification algorithms when classification alone is considered. Since our joint detection/recognition approach can directly detect nodules and classify its malignancy instead of performing the tasks separately, our approach is more practical for automatic cancer and nodules detection.

Revealing Tumor Habitats from Texture Heterogeneity Analysis for Classification of Lung Cancer Malignancy and Aggressiveness

  • Cherezov, Dmitry
  • Goldgof, Dmitry
  • Hall, Lawrence
  • Gillies, Robert
  • Schabath, Matthew
  • Müller, Henning
  • Depeursinge, Adrien
Sci RepScientific reports 2019 Journal Article, cited 0 times
Website
We propose an approach for characterizing structural heterogeneity of lung cancer nodules using Computed Tomography Texture Analysis (CTTA). Measures of heterogeneity were used to test the hypothesis that heterogeneity can be used as predictor of nodule malignancy and patient survival. To do this, we use the National Lung Screening Trial (NLST) dataset to determine if heterogeneity can represent differences between nodules in lung cancer and nodules in non-lung cancer patients. 253 participants are in the training set and 207 participants in the test set. To discriminate cancerous from non-cancerous nodules at the time of diagnosis, a combination of heterogeneity and radiomic features were evaluated to produce the best area under receiver operating characteristic curve (AUROC) of 0.85 and accuracy 81.64%. Second, we tested the hypothesis that heterogeneity can predict patient survival. We analyzed 40 patients diagnosed with lung adenocarcinoma (20 short-term and 20 long-term survival patients) using a leave-one-out cross validation approach for performance evaluation. A combination of heterogeneity features and radiomic features produce an AUROC of 0.9 and an accuracy of 85% to discriminate long- and short-term survivors.

Computed Tomography (CT) Image Quality Enhancement via a Uniform Framework Integrating Noise Estimation and Super-Resolution Networks

  • Chi, Jianning
  • Zhang, Yifei
  • Yu, Xiaosheng
  • Wang, Ying
  • Wu, Chengdong
Sensors (Basel) 2019 Journal Article, cited 2 times
Website
Computed tomography (CT) imaging technology has been widely used to assist medical diagnosis in recent years. However, noise during the process of imaging, and data compression during the process of storage and transmission always interrupt the image quality, resulting in unreliable performance of the post-processing steps in the computer assisted diagnosis system (CADs), such as medical image segmentation, feature extraction, and medical image classification. Since the degradation of medical images typically appears as noise and low-resolution blurring, in this paper, we propose a uniform deep convolutional neural network (DCNN) framework to handle the de-noising and super-resolution of the CT image at the same time. The framework consists of two steps: Firstly, a dense-inception network integrating an inception structure and dense skip connection is proposed to estimate the noise level. The inception structure is used to extract the noise and blurring features with respect to multiple receptive fields, while the dense skip connection can reuse those extracted features and transfer them across the network. Secondly, a modified residual-dense network combined with joint loss is proposed to reconstruct the high-resolution image with low noise. The inception block is applied on each skip connection of the dense-residual network so that the structure features of the image are transferred through the network more than the noise and blurring features. Moreover, both the perceptual loss and the mean square error (MSE) loss are used to restrain the network, leading to better performance in the reconstruction of image edges and details. Our proposed network integrates the degradation estimation, noise removal, and image super-resolution in one uniform framework to enhance medical image quality. We apply our method to the Cancer Imaging Archive (TCIA) public dataset to evaluate its ability in medical image quality enhancement. The experimental results demonstrate that the proposed method outperforms the state-of-the-art methods on de-noising and super-resolution by providing higher peak signal to noise ratio (PSNR) and structure similarity index (SSIM) values.

SVM-PUK Kernel Based MRI-brain Tumor Identification Using Texture and Gabor Wavelets

  • Chinnam, Siva
  • Sistla, Venkatramaphanikumar
  • Kolli, Venkata
Traitement du Signal 2019 Journal Article, cited 0 times
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Imaging phenotypes of breast cancer heterogeneity in pre-operative breast Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI) scans predict 10-year recurrence

  • Chitalia, Rhea
  • Rowland, Jennifer
  • McDonald, Elizabeth S
  • Pantalone, Lauren
  • Cohen, Eric A
  • Gastounioti, Aimilia
  • Feldman, Michael
  • Schnall, Mitchell
  • Conant, Emily
  • Kontos, Despina
Clinical Cancer Research 2019 Journal Article, cited 0 times
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Volume-based inter difference XOR pattern: a new pattern for pulmonary nodule detection in CT images

  • Chitradevi, A.
  • Singh, N. Nirmal
  • Jayapriya, K.
International Journal of Biomedical Engineering and Technology 2021 Journal Article, cited 0 times
Website
The pulmonary nodule identification which paves the path to the cancer diagnosis is a challenging task today. The proposed work, volume-based inter difference XOR pattern (VIDXP) provides an efficient lung nodule detection system using a 3D texture-based pattern which is formed by XOR pattern calculation of inter-frame grey value differences among centre frame with its neighbourhood frames in rotationally clockwise direction, for every segmented nodule. Different classifiers such as random forest (RF), decision tree (DT) and AdaBoost are used with ten trails of five-fold cross validation test for classification. The experimental analysis in the public database, lung image database consortium-image database resource initiative (LIDC-IDRI) shows that proposed scheme gives better accuracy while comparing with existing approaches. Further, the proposed scheme is enhanced by combining shape information using histogram of oriented gradient (HOG) which improves the classification accuracy.

Classification of the glioma grading using radiomics analysis

  • Cho, Hwan-ho
  • Lee, Seung-hak
  • Kim, Jonghoon
  • Park, Hyunjin
PeerJ 2018 Journal Article, cited 0 times
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Integrative analysis of imaging and transcriptomic data of the immune landscape associated with tumor metabolism in lung adenocarcinoma: Clinical and prognostic implications

  • Choi, Hongyoon
  • Na, Kwon Joong
THERANOSTICS 2018 Journal Article, cited 0 times
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A Cascaded Neural Network for Staging in Non-Small Cell Lung Cancer Using Pre-Treatment CT

  • Choi, J.
  • Cho, H. H.
  • Kwon, J.
  • Lee, H. Y.
  • Park, H.
Diagnostics (Basel) 2021 Journal Article, cited 0 times
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BACKGROUND AND AIM: Tumor staging in non-small cell lung cancer (NSCLC) is important for treatment and prognosis. Staging involves expert interpretation of imaging, which we aim to automate with deep learning (DL). We proposed a cascaded DL method comprised of two steps to classification between early- and advanced-stage NSCLC using pretreatment computed tomography. METHODS: We developed and tested a DL model to classify between early- and advanced-stage using training (n = 90), validation (n = 8), and two test (n = 37, n = 26) cohorts obtained from the public domain. The first step adopted an autoencoder network to compress the imaging data into latent variables and the second step used the latent variable to classify the stages using the convolutional neural network (CNN). Other DL and machine learning-based approaches were compared. RESULTS: Our model was tested in two test cohorts of CPTAC and TCGA. In CPTAC, our model achieved accuracy of 0.8649, sensitivity of 0.8000, specificity of 0.9412, and area under the curve (AUC) of 0.8206 compared to other approaches (AUC 0.6824-0.7206) for classifying between early- and advanced-stages. In TCGA, our model achieved accuracy of 0.8077, sensitivity of 0.7692, specificity of 0.8462, and AUC of 0.8343. CONCLUSION: Our cascaded DL model for classification NSCLC patients into early-stage and advanced-stage showed promising results and could help future NSCLC research.

Reproducible and Interpretable Spiculation Quantification for Lung Cancer Screening

  • Choi, Wookjin
  • Nadeem, Saad
  • Alam, Sadegh R.
  • Deasy, Joseph O.
  • Tannenbaum, Allen
  • Lu, Wei
Computer Methods and Programs in Biomedicine 2020 Journal Article, cited 0 times
Website
Spiculations are important predictors of lung cancer malignancy, which are spikes on the surface of the pulmonary nodules. In this study, we proposed an interpretable and parameter-free technique to quantify the spiculation using area distortion metric obtained by the conformal (angle-preserving) spherical parameterization. We exploit the insight that for an angle-preserved spherical mapping of a given nodule, the corresponding negative area distortion precisely characterizes the spiculations on that nodule. We introduced novel spiculation scores based on the area distortion metric and spiculation measures. We also semi-automatically segment lung nodule (for reproducibility) as well as vessel and wall attachment to differentiate the real spiculations from lobulation and attachment. A simple pathological malignancy prediction model is also introduced. We used the publicly-available LIDC-IDRI dataset pathologists (strong-label) and radiologists (weak-label) ratings to train and test radiomics models containing this feature, and then externally validate the models. We achieved AUC = 0.80 and 0.76, respectively, with the models trained on the 811 weakly-labeled LIDC datasets and tested on the 72 strongly-labeled LIDC and 73 LUNGx datasets; the previous best model for LUNGx had AUC = 0.68. The number-of-spiculations feature was found to be highly correlated (Spearman’s rank correlation coefficient ) with the radiologists’ spiculation score. We developed a reproducible and interpretable, parameter-free technique for quantifying spiculations on nodules. The spiculation quantification measures was then applied to the radiomics framework for pathological malignancy prediction with reproducible semi-automatic segmentation of nodule. Using our interpretable features (size, attachment, spiculation, lobulation), we were able to achieve higher performance than previous models. In the future, we will exhaustively test our model for lung cancer screening in the clinic.

Prediction of Human Papillomavirus Status and Overall Survival in Patients with Untreated Oropharyngeal Squamous Cell Carcinoma: Development and Validation of CT-Based Radiomics

  • Choi, Y.
  • Nam, Y.
  • Jang, J.
  • Shin, N. Y.
  • Ahn, K. J.
  • Kim, B. S.
  • Lee, Y. S.
  • Kim, M. S.
AJNR Am J Neuroradiol 2020 Journal Article, cited 0 times
Website
BACKGROUND AND PURPOSE: Human papillomavirus is a prognostic marker for oropharyngeal squamous cell carcinoma. We aimed to determine the value of CT-based radiomics for predicting the human papillomavirus status and overall survival in patients with oropharyngeal squamous cell carcinoma. MATERIALS AND METHODS: Eighty-six patients with oropharyngeal squamous cell carcinoma were retrospectively collected and grouped into training (n = 61) and test (n = 25) sets. For human papillomavirus status and overall survival prediction, radiomics features were selected via a random forest-based algorithm and Cox regression analysis, respectively. Relevant features were used to build multivariate Cox regression models and calculate the radiomics score. Human papillomavirus status and overall survival prediction were assessed via the area under the curve and concordance index, respectively. The models were validated in the test and The Cancer Imaging Archive cohorts (n = 78). RESULTS: For prediction of human papillomavirus status, radiomics features yielded areas under the curve of 0.865, 0.747, and 0.834 in the training, test, and validation sets, respectively. In the univariate Cox regression, the human papillomavirus status (positive: hazard ratio, 0.257; 95% CI, 0.09-0.7; P = .008), T-stage (>/=III: hazard ratio, 3.66; 95% CI, 1.34-9.99; P = .011), and radiomics score (high-risk: hazard ratio, 3.72; 95% CI, 1.21-11.46; P = .022) were associated with overall survival. The addition of the radiomics score to the clinical Cox model increased the concordance index from 0.702 to 0.733 (P = .01). Validation yielded concordance indices of 0.866 and 0.720. CONCLUSIONS: CT-based radiomics may be useful in predicting human papillomavirus status and overall survival in patients with oropharyngeal squamous cell carcinoma.

Machine learning and radiomic phenotyping of lower grade gliomas: improving survival prediction

  • Choi, Yoon Seong
  • Ahn, Sung Soo
  • Chang, Jong Hee
  • Kang, Seok-Gu
  • Kim, Eui Hyun
  • Kim, Se Hoon
  • Jain, Rajan
  • Lee, Seung-Koo
Eur Radiol 2020 Journal Article, cited 0 times
Website
BACKGROUND AND PURPOSE: Recent studies have highlighted the importance of isocitrate dehydrogenase (IDH) mutational status in stratifying biologically distinct subgroups of gliomas. This study aimed to evaluate whether MRI-based radiomic features could improve the accuracy of survival predictions for lower grade gliomas over clinical and IDH status. MATERIALS AND METHODS: Radiomic features (n = 250) were extracted from preoperative MRI data of 296 lower grade glioma patients from databases at our institutional (n = 205) and The Cancer Genome Atlas (TCGA)/The Cancer Imaging Archive (TCIA) (n = 91) datasets. For predicting overall survival, random survival forest models were trained with radiomic features; non-imaging prognostic factors including age, resection extent, WHO grade, and IDH status on the institutional dataset, and validated on the TCGA/TCIA dataset. The performance of the random survival forest (RSF) model and incremental value of radiomic features were assessed by time-dependent receiver operating characteristics. RESULTS: The radiomics RSF model identified 71 radiomic features to predict overall survival, which were successfully validated on TCGA/TCIA dataset (iAUC, 0.620; 95% CI, 0.501-0.756). Relative to the RSF model from the non-imaging prognostic parameters, the addition of radiomic features significantly improved the overall survival prediction accuracy of the random survival forest model (iAUC, 0.627 vs. 0.709; difference, 0.097; 95% CI, 0.003-0.209). CONCLUSION: Radiomic phenotyping with machine learning can improve survival prediction over clinical profile and genomic data for lower grade gliomas. KEY POINTS: * Radiomics analysis with machine learning can improve survival prediction over the non-imaging factors (clinical and molecular profiles) for lower grade gliomas, across different institutions.

Incremental Prognostic Value of ADC Histogram Analysis over MGMT Promoter Methylation Status in Patients with Glioblastoma

  • Choi, Yoon Seong
  • Ahn, Sung Soo
  • Kim, Dong Wook
  • Chang, Jong Hee
  • Kang, Seok-Gu
  • Kim, Eui Hyun
  • Kim, Se Hoon
  • Rim, Tyler Hyungtaek
  • Lee, Seung-Koo
RadiologyRadiology 2016 Journal Article, cited 18 times
Website
Purpose To investigate the incremental prognostic value of apparent diffusion coefficient (ADC) histogram analysis over oxygen 6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status in patients with glioblastoma and the correlation between ADC parameters and MGMT status. Materials and Methods This retrospective study was approved by institutional review board, and informed consent was waived. A total of 112 patients with glioblastoma were divided into training (74 patients) and test (38 patients) sets. Overall survival (OS) and progression-free survival (PFS) was analyzed with ADC parameters, MGMT status, and other clinical factors. Multivariate Cox regression models with and without ADC parameters were constructed. Model performance was assessed with c index and receiver operating characteristic curve analyses for 12- and 16-month OS and 12-month PFS in the training set and validated in the test set. ADC parameters were compared according to MGMT status for the entire cohort. Results By using ADC parameters, the c indices and diagnostic accuracies for 12- and 16-month OS and 12-month PFS in the models showed significant improvement, with the exception of c indices in the models for PFS (P < .05 for all) in the training set. In the test set, the diagnostic accuracy was improved by using ADC parameters and was significant, with the 25th and 50th percentiles of ADC for 16-month OS (P = .040 and P = .047) and the 25th percentile of ADC for 12-month PFS (P = .026). No significant correlation was found between ADC parameters and MGMT status. Conclusion ADC histogram analysis had incremental prognostic value over MGMT promoter methylation status in patients with glioblastoma. ((c)) RSNA, 2016 Online supplemental material is available for this article.

ST3GAL1-associated transcriptomic program in glioblastoma tumor growth, invasion, and prognosis

  • Chong, Yuk Kien
  • Sandanaraj, Edwin
  • Koh, Lynnette WH
  • Thangaveloo, Moogaambikai
  • Tan, Melanie SY
  • Koh, Geraldene RH
  • Toh, Tan Boon
  • Lim, Grace GY
  • Holbrook, Joanna D
  • Kon, Oi Lian
  • Nadarajah, M.
  • Ng, I.
  • Ng, W. H.
  • Tan, N. S.
  • Lim, K. L.
  • Tang, C.
  • Ang, B. T.
2016 Journal Article, cited 16 times
Website
BACKGROUND: Cell surface sialylation is associated with tumor cell invasiveness in many cancers. Glioblastoma is the most malignant primary brain tumor and is highly infiltrative. ST3GAL1 sialyltransferase gene is amplified in a subclass of glioblastomas, and its role in tumor cell self-renewal remains unexplored. METHODS: Self-renewal of patient glioma cells was evaluated using clonogenic, viability, and invasiveness assays. ST3GAL1 was identified from differentially expressed genes in Peanut Agglutinin-stained cells and validated in REMBRANDT (n = 390) and Gravendeel (n = 276) clinical databases. Gene set enrichment analysis revealed upstream processes. TGFbeta signaling on ST3GAL1 transcription was assessed using chromatin immunoprecipitation. Transcriptome analysis of ST3GAL1 knockdown cells was done to identify downstream pathways. A constitutively active FoxM1 mutant lacking critical anaphase-promoting complex/cyclosome ([APC/C]-Cdh1) binding sites was used to evaluate ST3Gal1-mediated regulation of FoxM1 protein. Finally, the prognostic role of ST3Gal1 was determined using an orthotopic xenograft model (3 mice groups comprising nontargeting and 2 clones of ST3GAL1 knockdown in NNI-11 [8 per group] and NNI-21 [6 per group]), and the correlation with patient clinical information. All statistical tests on patients' data were two-sided; other P values below are one-sided. RESULTS: High ST3GAL1 expression defines an invasive subfraction with self-renewal capacity; its loss of function prolongs survival in a mouse model established from mesenchymal NNI-11 (P < .001; groups of 8 in 3 arms: nontargeting, C1, and C2 clones of ST3GAL1 knockdown). ST3GAL1 transcriptomic program stratifies patient survival (hazard ratio [HR] = 2.47, 95% confidence interval [CI] = 1.72 to 3.55, REMBRANDT P = 1.92 x 10(-)(8); HR = 2.89, 95% CI = 1.94 to 4.30, Gravendeel P = 1.05 x 10(-)(1)(1)), independent of age and histology, and associates with higher tumor grade and T2 volume (P = 1.46 x 10(-)(4)). TGFbeta signaling, elevated in mesenchymal patients, correlates with high ST3GAL1 (REMBRANDT gliomacor = 0.31, P = 2.29 x 10(-)(1)(0); Gravendeel gliomacor = 0.50, P = 3.63 x 10(-)(2)(0)). The transcriptomic program upon ST3GAL1 knockdown enriches for mitotic cell cycle processes. FoxM1 was identified as a statistically significantly modulated gene (P = 2.25 x 10(-)(5)) and mediates ST3Gal1 signaling via the (APC/C)-Cdh1 complex. CONCLUSIONS: The ST3GAL1-associated transcriptomic program portends poor prognosis in glioma patients and enriches for higher tumor grades of the mesenchymal molecular classification. We show that ST3Gal1-regulated self-renewal traits are crucial to the sustenance of glioblastoma multiforme growth.

Application of Artificial Neural Networks for Prognostic Modeling in Lung Cancer after Combining Radiomic and Clinical Features

  • Chufal, Kundan S.
  • Ahmad, Irfan
  • Pahuja, Anjali K.
  • Miller, Alexis A.
  • Singh, Rajpal
  • Chowdhary, Rahul L.
Asian Journal of Oncology 2019 Journal Article, cited 0 times
Website
Objective This study was aimed to investigate machine learning (ML) and artificial neural networks (ANNs) in the prognostic modeling of lung cancer, utilizing high-dimensional data. Materials and Methods A computed tomography (CT) dataset of inoperable nonsmall cell lung carcinoma (NSCLC) patients with embedded tumor segmentation and survival status, comprising 422 patients, was selected. Radiomic data extraction was performed on Computation Environment for Radiation Research (CERR). The survival probability was first determined based on clinical features only and then unsupervised ML methods. Supervised ANN modeling was performed by direct and hybrid modeling which were subsequently compared. Statistical significance was set at <0.05. Results Survival analyses based on clinical features alone were not significant, except for gender. ML clustering performed on unselected radiomic and clinical data demonstrated a significant difference in survival (two-step cluster, median overall survival [ mOS]: 30.3 vs. 17.2 m; p = 0.03; K-means cluster, mOS: 21.1 vs. 7.3 m; p < 0.001). Direct ANN modeling yielded a better overall model accuracy utilizing multilayer perceptron (MLP) than radial basis function (RBF; 79.2 vs. 61.4%, respectively). Hybrid modeling with MLP (after feature selection with ML) resulted in an overall model accuracy of 80%. There was no difference in model accuracy after direct and hybrid modeling (p = 0.164). Conclusion Our preliminary study supports the application of ANN in predicting outcomes based on radiomic and clinical data.

Results of initial low-dose computed tomographic screening for lung cancer

  • Church, T. R.
  • Black, W. C.
  • Aberle, D. R.
  • Berg, C. D.
  • Clingan, K. L.
  • Duan, F.
  • Fagerstrom, R. M.
  • Gareen, I. F.
  • Gierada, D. S.
  • Jones, G. C.
  • Mahon, I.
  • Marcus, P. M.
  • Sicks, J. D.
  • Jain, A.
  • Baum, S.
N Engl J MedThe New England journal of medicine 2013 Journal Article, cited 529 times
Website
BACKGROUND: Lung cancer is the largest contributor to mortality from cancer. The National Lung Screening Trial (NLST) showed that screening with low-dose helical computed tomography (CT) rather than with chest radiography reduced mortality from lung cancer. We describe the screening, diagnosis, and limited treatment results from the initial round of screening in the NLST to inform and improve lung-cancer-screening programs. METHODS: At 33 U.S. centers, from August 2002 through April 2004, we enrolled asymptomatic participants, 55 to 74 years of age, with a history of at least 30 pack-years of smoking. The participants were randomly assigned to undergo annual screening, with the use of either low-dose CT or chest radiography, for 3 years. Nodules or other suspicious findings were classified as positive results. This article reports findings from the initial screening examination. RESULTS: A total of 53,439 eligible participants were randomly assigned to a study group (26,715 to low-dose CT and 26,724 to chest radiography); 26,309 participants (98.5%) and 26,035 (97.4%), respectively, underwent screening. A total of 7191 participants (27.3%) in the low-dose CT group and 2387 (9.2%) in the radiography group had a positive screening result; in the respective groups, 6369 participants (90.4%) and 2176 (92.7%) had at least one follow-up diagnostic procedure, including imaging in 5717 (81.1%) and 2010 (85.6%) and surgery in 297 (4.2%) and 121 (5.2%). Lung cancer was diagnosed in 292 participants (1.1%) in the low-dose CT group versus 190 (0.7%) in the radiography group (stage 1 in 158 vs. 70 participants and stage IIB to IV in 120 vs. 112). Sensitivity and specificity were 93.8% and 73.4% for low-dose CT and 73.5% and 91.3% for chest radiography, respectively. CONCLUSIONS: The NLST initial screening results are consistent with the existing literature on screening by means of low-dose CT and chest radiography, suggesting that a reduction in mortality from lung cancer is achievable at U.S. screening centers that have staff experienced in chest CT. (Funded by the National Cancer Institute; NLST ClinicalTrials.gov number, NCT00047385.).

Automatic detection of spiculation of pulmonary nodules in computed tomography images

  • Ciompi, F
  • Jacobs, C
  • Scholten, ET
  • van Riel, SJ
  • Wille, MMW
  • Prokop, M
  • van Ginneken, B
2015 Conference Proceedings, cited 5 times
Website

Reproducing 2D breast mammography images with 3D printed phantoms

  • Clark, Matthew
  • Ghammraoui, Bahaa
  • Badal, Andreu
2016 Conference Proceedings, cited 2 times
Website

The Quantitative Imaging Network: NCI's Historical Perspective and Planned Goals

  • Clarke, Laurence P.
  • Nordstrom, Robert J.
  • Zhang, Huiming
  • Tandon, Pushpa
  • Zhang, Yantian
  • Redmond, George
  • Farahani, Keyvan
  • Kelloff, Gary
  • Henderson, Lori
  • Shankar, Lalitha
  • Deye, James
  • Capala, Jacek
  • Jacobs, Paula
Transl OncolTranslational oncology 2014 Journal Article, cited 0 times
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Using Machine Learning Applied to Radiomic Image Features for Segmenting Tumour Structures

  • Clifton, Henry
  • Vial, Alanna
  • Miller, Andrew
  • Ritz, Christian
  • Field, Matthew
  • Holloway, Lois
  • Ros, Montserrat
  • Carolan, Martin
  • Stirling, David
2019 Conference Paper, cited 0 times
Website
Lung cancer (LC) was the predicted leading causeof Australian cancer fatalities in 2018 (around 9,200 deaths). Non-Small Cell Lung Cancer (NSCLC) tumours with larger amounts of heterogeneity have been linked to a worse outcome.Medical imaging is widely used in oncology and non-invasively collects data about the whole tumour. The field of radiomics uses these medical images to extract quantitative image featuresand promises further understanding of the disease at the time of diagnosis, during treatment and in follow up. It is well known that manual and semi-automatic tumour segmentation methods are subject to inter-observer variability which reduces confidence in the treatment region and extentof disease. This leads to tumour under- and over-estimation which can impact on treatment outcome and treatment-induced morbidity.This research aims to use radiomic features centred at each pixel to segment the location of the lung tumour on Computed Tomography (CT) scans. To achieve this objective, a DecisionTree (DT) model was trained using sampled CT data from eight patients. The data consisted of 25 pixel-based texture features calculated from four Gray Level Matrices (GLMs)describing the region around each pixel. The model was assessed using an unseen patient through both a confusion matrix and interpretation of the segment.The findings showed that the model accurately (AUROC =83.9%) predicts tumour location within the test data, concluding that pixel based textural features likely contribute to segmenting the lung tumour. The prediction displayed a strong representation of the manually segmented Region of Interest (ROI), which is considered the ground truth for the purpose of this research.

Acute Lymphoblastic Leukemia Detection Using Depthwise Separable Convolutional Neural Networks

  • Clinton Jr, Laurence P
  • Somes, Karen M
  • Chu, Yongjun
  • Javed, Faizan
SMU Data Science Review 2020 Journal Article, cited 0 times
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Automated Medical Image Modality Recognition by Fusion of Visual and Text Information

  • Codella, Noel
  • Connell, Jonathan
  • Pankanti, Sharath
  • Merler, Michele
  • Smith, John R
2014 Book Section, cited 10 times
Website

Semantic Model Vector for ImageCLEF2013

  • Codella, Noel
  • Merler, Michele
2014 Report, cited 0 times
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Parallel Implementation of the DRLSE Algorithm

  • Coelho, Daniel Popp
  • Furuie, Sérgio Shiguemi
2020 Conference Proceedings, cited 0 times
Website
The Distance-Regularized Level Set Evolution (DRLSE) algorithm solves many problems that plague the class of Level Set algorithms, but has a significant computational cost and is sensitive to its many parameters. Configuring these parameters is a time-intensive trial-and-error task that limits the usability of the algorithm. This is especially true in the field of Medical Imaging, where it would be otherwise highly suitable. The aim of this work is to develop a parallel implementation of the algorithm using the Compute-Unified Device Architecture (CUDA) for Graphics Processing Units (GPU), which would reduce the computational cost of the algorithm, bringing it to the interactive regime. This would lessen the burden of configuring its parameters and broaden its application. Using consumer-grade, hardware, we observed performance gains between roughly 800% and 1700% when comparing against a purely serial C++ implementation we developed, and gains between roughly 180% and 500%, when comparing against the MATLAB reference implementation of DRLSE, both depending on input image resolution.

NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures

  • Colen, Rivka
  • Foster, Ian
  • Gatenby, Robert
  • Giger, Mary Ellen
  • Gillies, Robert
  • Gutman, David
  • Heller, Matthew
  • Jain, Rajan
  • Madabhushi, Anant
  • Madhavan, Subha
  • Napel, Sandy
  • Rao, Arvind
  • Saltz, Joel
  • Tatum, James
  • Verhaak, Roeland
  • Whitman, Gary
Transl OncolTranslational oncology 2014 Journal Article, cited 39 times
Website
The National Cancer Institute (NCI) Cancer Imaging Program organized two related workshops on June 26-27, 2013, entitled "Correlating Imaging Phenotypes with Genomics Signatures Research" and "Scalable Computational Resources as Required for Imaging-Genomics Decision Support Systems." The first workshop focused on clinical and scientific requirements, exploring our knowledge of phenotypic characteristics of cancer biological properties to determine whether the field is sufficiently advanced to correlate with imaging phenotypes that underpin genomics and clinical outcomes, and exploring new scientific methods to extract phenotypic features from medical images and relate them to genomics analyses. The second workshop focused on computational methods that explore informatics and computational requirements to extract phenotypic features from medical images and relate them to genomics analyses and improve the accessibility and speed of dissemination of existing NIH resources. These workshops linked clinical and scientific requirements of currently known phenotypic and genotypic cancer biology characteristics with imaging phenotypes that underpin genomics and clinical outcomes. The group generated a set of recommendations to NCI leadership and the research community that encourage and support development of the emerging radiogenomics research field to address short-and longer-term goals in cancer research.

Imaging genomic mapping of an invasive MRI phenotype predicts patient outcome and metabolic dysfunction: a TCGA glioma phenotype research group project

  • Colen, Rivka R
  • Vangel, Mark
  • Wang, Jixin
  • Gutman, David A
  • Hwang, Scott N
  • Wintermark, Max
  • Jain, Rajan
  • Jilwan-Nicolas, Manal
  • Chen, James Y
  • Raghavan, Prashant
  • Holder, C. A.
  • Rubin, D.
  • Huang, E.
  • Kirby, J.
  • Freymann, J.
  • Jaffe, C. C.
  • Flanders, A.
  • TCGA Glioma Phenotype Research Group
  • Zinn, P. O.
BMC Medical Genomics 2014 Journal Article, cited 47 times
Website
BACKGROUND: Invasion of tumor cells into adjacent brain parenchyma is a major cause of treatment failure in glioblastoma. Furthermore, invasive tumors are shown to have a different genomic composition and metabolic abnormalities that allow for a more aggressive GBM phenotype and resistance to therapy. We thus seek to identify those genomic abnormalities associated with a highly aggressive and invasive GBM imaging-phenotype. METHODS: We retrospectively identified 104 treatment-naive glioblastoma patients from The Cancer Genome Atlas (TCGA) whom had gene expression profiles and corresponding MR imaging available in The Cancer Imaging Archive (TCIA). The standardized VASARI feature-set criteria were used for the qualitative visual assessments of invasion. Patients were assigned to classes based on the presence (Class A) or absence (Class B) of statistically significant invasion parameters to create an invasive imaging signature; imaging genomic analysis was subsequently performed using GenePattern Comparative Marker Selection module (Broad Institute). RESULTS: Our results show that patients with a combination of deep white matter tracts and ependymal invasion (Class A) on imaging had a significant decrease in overall survival as compared to patients with absence of such invasive imaging features (Class B) (8.7 versus 18.6 months, p < 0.001). Mitochondrial dysfunction was the top canonical pathway associated with Class A gene expression signature. The MYC oncogene was predicted to be the top activation regulator in Class A. CONCLUSION: We demonstrate that MRI biomarker signatures can identify distinct GBM phenotypes associated with highly significant survival differences and specific molecular pathways. This study identifies mitochondrial dysfunction as the top canonical pathway in a very aggressive GBM phenotype. Thus, imaging-genomic analyses may prove invaluable in detecting novel targetable genomic pathways.

Glioblastoma: Imaging Genomic Mapping Reveals Sex-specific Oncogenic Associations of Cell Death

  • Colen, Rivka R
  • Wang, Jixin
  • Singh, Sanjay K
  • Gutman, David A
  • Zinn, Pascal O
RadiologyRadiology 2014 Journal Article, cited 36 times
Website
PURPOSE: To identify the molecular profiles of cell death as defined by necrosis volumes at magnetic resonance (MR) imaging and uncover sex-specific molecular signatures potentially driving oncogenesis and cell death in glioblastoma (GBM). MATERIALS AND METHODS: This retrospective study was HIPAA compliant and had institutional review board approval, with waiver of the need to obtain informed consent. The molecular profiles for 99 patients (30 female patients, 69 male patients) were identified from the Cancer Genome Atlas, and quantitative MR imaging data were obtained from the Cancer Imaging Archive. Volumes of necrosis at MR imaging were extracted. Differential gene expression profiles were obtained in those patients (including male and female patients separately) with high versus low MR imaging volumes of tumor necrosis. Ingenuity Pathway Analysis was used for messenger RNA-microRNA interaction analysis. A histopathologic data set (n = 368; 144 female patients, 224 male patients) was used to validate the MR imaging findings by assessing the amount of cell death. A connectivity map was used to identify therapeutic agents potentially targeting sex-specific cell death in GBM. RESULTS: Female patients showed significantly lower volumes of necrosis at MR imaging than male patients (6821 vs 11 050 mm(3), P = .03). Female patients, unlike male patients, with high volumes of necrosis at imaging had significantly shorter survival (6.5 vs 14.5 months, P = .01). Transcription factor analysis suggested that cell death in female patients with GBM is associated with MYC, while that in male patients is associated with TP53 activity. Additionally, a group of therapeutic agents that can potentially be tested to target cell death in a sex-specific manner was identified. CONCLUSION: The results of this study suggest that cell death in GBM may be driven by sex-specific molecular pathways.

A Framework for Customizable FPGA-based Image Registration Accelerators

  • Conficconi, Davide
  • D'Arnese, Eleonora
  • Del Sozzo, Emanuele
  • Sciuto, Donatella
  • Santambrogio, Marco D.
2021 Conference Proceedings, cited 0 times
Website
Image Registration is a highly compute-intensive optimization procedure that determines the geometric transformation to align a floating image to a reference one. Generally, the registration targets are images taken from different time instances, acquisition angles, and/or sensor types. Several methodologies are employed in the literature to address the limiting factors of this class of algorithms, among which hardware accelerators seem the most promising solution to boost performance. However, most hardware implementations are either closed-source or tailored to a specific context, limiting their application to different fields. For these reasons, we propose an open-source hardware-software framework to generate a configurable architecture for the most compute-intensive part of registration algorithms, namely the similarity metric computation. This metric is the Mutual Information, a well-known calculus from the Information Theory, used in several optimization procedures. Through different design parameters configurations, we explore several design choices of our highly-customizable architecture and validate it on multiple FPGAs. We evaluated various architectures against an optimized Matlab implementation on an Intel Xeon Gold, reaching a speedup up to 2.86x, and remarkable performance and power efficiency against other state-of-the-art approaches.

The exceptional responders initiative: feasibility of a National Cancer Institute pilot study

  • Conley, Barbara A
  • Staudt, Lou
  • Takebe, Naoko
  • Wheeler, David A
  • Wang, Linghua
  • Cardenas, Maria F
  • Korchina, Viktoriya
  • Zenklusen, Jean Claude
  • McShane, Lisa M
  • Tricoli, James V
JNCI: Journal of the National Cancer Institute 2021 Journal Article, cited 5 times
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Extended Modality Propagation: Image Synthesis of Pathological Cases

  • N. Cordier
  • H. Delingette
  • M. Le
  • N. Ayache
IEEE Transactions on Medical Imaging 2016 Journal Article, cited 18 times
Website

Combined Megavoltage and Contrast-Enhanced Radiotherapy as an Intrafraction Motion Management Strategy in Lung SBRT

  • Coronado-Delgado, Daniel A
  • Garnica-Garza, Hector M
Technol Cancer Res Treat 2019 Journal Article, cited 0 times
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Using Monte Carlo simulation and a realistic patient model, it is shown that the volume of healthy tissue irradiated at therapeutic doses can be drastically reduced using a combination of standard megavoltage and kilovoltage X-ray beams with a contrast agent previously loaded into the tumor, without the need to reduce standard treatment margins. Four-dimensional computed tomography images of 2 patients with a centrally located and a peripherally located tumor were obtained from a public database and subsequently used to plan robotic stereotactic body radiotherapy treatments. Two modalities are assumed: conventional high-energy stereotactic body radiotherapy and a treatment with contrast agent loaded in the tumor and a kilovoltage X-ray beam replacing the megavoltage beam (contrast-enhanced radiotherapy). For each patient model, 2 planning target volumes were designed: one following the recommendations from either Radiation Therapy Oncology Group (RTOG) 0813 or RTOG 0915 task group depending on the patient model and another with a 2-mm uniform margin determined solely on beam penumbra considerations. The optimized treatments with RTOG margins were imparted to the moving phantom to model the dose distribution that would be obtained as a result of intrafraction motion. Treatment plans are then compared to the plan with the 2-mm uniform margin considered to be the ideal plan. It is shown that even for treatments in which only one-fifth of the total dose is imparted via the contrast-enhanced radiotherapy modality and with the use of standard treatment margins, the resultant absorbed dose distributions are such that the volume of healthy tissue irradiated to high doses is close to what is obtained under ideal conditions.

Bayesian Kernel Models for Statistical Genetics and Cancer Genomics

  • Crawford, Lorin
2017 Thesis, cited 0 times

StaticCodeCT: single coded aperture tensorial X-ray CT

  • Cuadros, A. P.
  • Ma, X.
  • Restrepo, C. M.
  • Arce, G. R.
Opt Express 2021 Journal Article, cited 0 times
Website
Coded aperture X-ray CT (CAXCT) is a new low-dose imaging technology that promises far-reaching benefits in industrial and clinical applications. It places various coded apertures (CA) at a time in front of the X-ray source to partially block the radiation. The ill-posed inverse reconstruction problem is then solved using l1-norm-based iterative reconstruction methods. Unfortunately, to attain high-quality reconstructions, the CA patterns must change in concert with the view-angles making the implementation impractical. This paper proposes a simple yet radically different approach to CAXCT, which is coined StaticCodeCT, that uses a single-static CA in the CT gantry, thus making the imaging system amenable for practical implementations. Rather than using conventional compressed sensing algorithms for recovery, we introduce a new reconstruction framework for StaticCodeCT. Namely, we synthesize the missing measurements using low-rank tensor completion principles that exploit the multi-dimensional data correlation and low-rank nature of a 3-way tensor formed by stacking the 2D coded CT projections. Then, we use the FDK algorithm to recover the 3D object. Computational experiments using experimental projection measurements exhibit up to 10% gains in the normalized root mean square distance of the reconstruction using the proposed method compared with those attained by alternative low-dose systems.

Predicting the ISUP grade of clear cell renal cell carcinoma with multiparametric MR and multiphase CT radiomics

  • Cui, Enming
  • Li, Zhuoyong
  • Ma, Changyi
  • Li, Qing
  • Lei, Yi
  • Lan, Yong
  • Yu, Juan
  • Zhou, Zhipeng
  • Li, Ronggang
  • Long, Wansheng
  • Lin, Fan
Eur Radiol 2020 Journal Article, cited 0 times
Website
OBJECTIVE: To investigate externally validated magnetic resonance (MR)-based and computed tomography (CT)-based machine learning (ML) models for grading clear cell renal cell carcinoma (ccRCC). MATERIALS AND METHODS: Patients with pathologically proven ccRCC in 2009-2018 were retrospectively included for model development and internal validation; patients from another independent institution and The Cancer Imaging Archive dataset were included for external validation. Features were extracted from T1-weighted, T2-weighted, corticomedullary-phase (CMP), and nephrographic-phase (NP) MR as well as precontrast-phase (PCP), CMP, and NP CT. CatBoost was used for ML-model investigation. The reproducibility of texture features was assessed using intraclass correlation coefficient (ICC). Accuracy (ACC) was used for ML-model performance evaluation. RESULTS: Twenty external and 440 internal cases were included. Among 368 and 276 texture features from MR and CT, 322 and 250 features with good to excellent reproducibility (ICC >/= 0.75) were included for ML-model development. The best MR- and CT-based ML models satisfactorily distinguished high- from low-grade ccRCCs in internal (MR-ACC = 73% and CT-ACC = 79%) and external (MR-ACC = 74% and CT-ACC = 69%) validation. Compared to single-sequence or single-phase images, the classifiers based on all-sequence MR (71% to 73% in internal and 64% to 74% in external validation) and all-phase CT (77% to 79% in internal and 61% to 69% in external validation) images had significant increases in ACC. CONCLUSIONS: MR- and CT-based ML models are valuable noninvasive techniques for discriminating high- from low-grade ccRCCs, and multiparameter MR- and multiphase CT-based classifiers are potentially superior to those based on single-sequence or single-phase imaging. KEY POINTS: * Both the MR- and CT-based machine learning models are reliable predictors for differentiating high- from low-grade ccRCCs. * ML models based on multiparameter MR sequences and multiphase CT images potentially outperform those based on single-sequence or single-phase images in ccRCC grading.

Primary lung tumor segmentation from PET–CT volumes with spatial–topological constraint

  • Cui, Hui
  • Wang, Xiuying
  • Lin, Weiran
  • Zhou, Jianlong
  • Eberl, Stefan
  • Feng, Dagan
  • Fulham, Michael
International Journal of Computer Assisted Radiology and Surgery 2016 Journal Article, cited 14 times
Website

Volume of high-risk intratumoral subregions at multi-parametric MR imaging predicts overall survival and complements molecular analysis of glioblastoma

  • Cui, Yi
  • Ren, Shangjie
  • Tha, Khin Khin
  • Wu, Jia
  • Shirato, Hiroki
  • Li, Ruijiang
European Radiology 2017 Journal Article, cited 10 times
Website

Prognostic Imaging Biomarkers in Glioblastoma: Development and Independent Validation on the Basis of Multiregion and Quantitative Analysis of MR Images

  • Cui, Yi
  • Tha, Khin Khin
  • Terasaka, Shunsuke
  • Yamaguchi, Shigeru
  • Wang, Jeff
  • Kudo, Kohsuke
  • Xing, Lei
  • Shirato, Hiroki
  • Li, Ruijiang
RadiologyRadiology 2015 Journal Article, cited 45 times
Website
PURPOSE: To develop and independently validate prognostic imaging biomarkers for predicting survival in patients with glioblastoma on the basis of multiregion quantitative image analysis. MATERIALS AND METHODS: This retrospective study was approved by the local institutional review board, and informed consent was waived. A total of 79 patients from two independent cohorts were included. The discovery and validation cohorts consisted of 46 and 33 patients with glioblastoma from the Cancer Imaging Archive (TCIA) and the local institution, respectively. Preoperative T1-weighted contrast material-enhanced and T2-weighted fluid-attenuation inversion recovery magnetic resonance (MR) images were analyzed. For each patient, we semiautomatically delineated the tumor and performed automated intratumor segmentation, dividing the tumor into spatially distinct subregions that demonstrate coherent intensity patterns across multiparametric MR imaging. Within each subregion and for the entire tumor, we extracted quantitative imaging features, including those that fully capture the differential contrast of multimodality MR imaging. A multivariate sparse Cox regression model was trained by using TCIA data and tested on the validation cohort. RESULTS: The optimal prognostic model identified five imaging biomarkers that quantified tumor surface area and intensity distributions of the tumor and its subregions. In the validation cohort, our prognostic model achieved a concordance index of 0.67 and significant stratification of overall survival by using the log-rank test (P = .018), which outperformed conventional prognostic factors, such as age (concordance index, 0.57; P = .389) and tumor volume (concordance index, 0.59; P = .409). CONCLUSION: The multiregion analysis presented here establishes a general strategy to effectively characterize intratumor heterogeneity manifested at multimodality imaging and has the potential to reveal useful prognostic imaging biomarkers in glioblastoma.

Deep Learning Whole-Gland and Zonal Prostate Segmentation on a Public MRI Dataset

  • Cuocolo, Renato
  • Comelli, Albert
  • Stefano, Alessandro
  • Benfante, Viviana
  • Dahiya, Navdeep
  • Stanzione, Arnaldo
  • Castaldo, Anna
  • De Lucia, Davide Raffaele
  • Yezzi, Anthony
  • Imbriaco, Massimo
Journal of Magnetic Resonance Imaging 2021 Journal Article, cited 0 times
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Background Prostate volume, as determined by magnetic resonance imaging (MRI), is a useful biomarker both for distinguishing between benign and malignant pathology and can be used either alone or combined with other parameters such as prostate-specific antigen. Purpose This study compared different deep learning methods for whole-gland and zonal prostate segmentation. Study Type Retrospective. Population A total of 204 patients (train/test = 99/105) from the PROSTATEx public dataset. Field strength/Sequence A 3 T, TSE T2-weighted. Assessment Four operators performed manual segmentation of the whole-gland, central zone + anterior stroma + transition zone (TZ), and peripheral zone (PZ). U-net, efficient neural network (ENet), and efficient residual factorized ConvNet (ERFNet) were trained and tuned on the training data through 5-fold cross-validation to segment the whole gland and TZ separately, while PZ automated masks were obtained by the subtraction of the first two. Statistical Tests Networks were evaluated on the test set using various accuracy metrics, including the Dice similarity coefficient (DSC). Model DSC was compared in both the training and test sets using the analysis of variance test (ANOVA) and post hoc tests. Parameter number, disk size, training, and inference times determined network computational complexity and were also used to assess the model performance differences. A P < 0.05 was selected to indicate the statistical significance. Results The best DSC (P < 0.05) in the test set was achieved by ENet: 91% ± 4% for the whole gland, 87% ± 5% for the TZ, and 71% ± 8% for the PZ. U-net and ERFNet obtained, respectively, 88% ± 6% and 87% ± 6% for the whole gland, 86% ± 7% and 84% ± 7% for the TZ, and 70% ± 8% and 65 ± 8% for the PZ. Training and inference time were lowest for ENet. Data Conclusion Deep learning networks can accurately segment the prostate using T2-weighted images. Evidence Level 4 Technical Efficacy Stage 2

Quality control and whole-gland, zonal and lesion annotations for the PROSTATEx challenge public dataset

  • Cuocolo, R.
  • Stanzione, A.
  • Castaldo, A.
  • De Lucia, D. R.
  • Imbriaco, M.
Eur J Radiol 2021 Journal Article, cited 0 times
Website
PURPOSE: Radiomic features are promising quantitative parameters that can be extracted from medical images and employed to build machine learning predictive models. However, generalizability is a key concern, encouraging the use of public image datasets. We performed a quality assessment of the PROSTATEx training dataset and provide publicly available lesion, whole-gland, and zonal anatomy segmentation masks. METHOD: Two radiology residents and two experienced board-certified radiologists reviewed the 204 prostate MRI scans (330 lesions) included in the training dataset. The quality of provided lesion coordinate was scored using the following scale: 0 = perfectly centered, 1 = within lesion, 2 = within the prostate without lesion, 3 = outside the prostate. All clearly detectable lesions were segmented individually slice-by-slice on T2-weighted and apparent diffusion coefficient images. With the same methodology, volumes of interest including the whole gland, transition, and peripheral zones were annotated. RESULTS: Of the 330 available lesion identifiers, 3 were duplicates (1%). From the remaining, 218 received score = 0, 74 score = 1, 31 score = 2 and 4 score = 3. Overall, 299 lesions were verified and segmented. Independently of lesion coordinate score and other issues (e.g., lesion coordinates falling outside DICOM images, artifacts etc.), the whole prostate gland and zonal anatomy were also manually annotated for all cases. CONCLUSION: While several issues were encountered evaluating the original PROSTATEx dataset, the improved quality and availability of lesion, whole-gland and zonal segmentations will increase its potential utility as a common benchmark in prostate MRI radiomics.

Tumor Transcriptome Reveals High Expression of IL-8 in Non-Small Cell Lung Cancer Patients with Low Pectoralis Muscle Area and Reduced Survival

  • Cury, Sarah Santiloni
  • de Moraes, Diogo
  • Freire, Paula Paccielli
  • de Oliveira, Grasieli
  • Marques, Douglas Venancio Pereira
  • Fernandez, Geysson Javier
  • Dal-Pai-Silva, Maeli
  • Hasimoto, Erica Nishida
  • Dos Reis, Patricia Pintor
  • Rogatto, Silvia Regina
  • Carvalho, Robson Francisco
Cancers (Basel) 2019 Journal Article, cited 1 times
Website
Cachexia is a syndrome characterized by an ongoing loss of skeletal muscle mass associated with poor patient prognosis in non-small cell lung cancer (NSCLC). However, prognostic cachexia biomarkers in NSCLC are unknown. Here, we analyzed computed tomography (CT) images and tumor transcriptome data to identify potentially secreted cachexia biomarkers (PSCB) in NSCLC patients with low-muscularity. We integrated radiomics features (pectoralis muscle, sternum, and tenth thoracic (T10) vertebra) from CT of 89 NSCLC patients, which allowed us to identify an index for screening muscularity. Next, a tumor transcriptomic-based secretome analysis from these patients (discovery set) was evaluated to identify potential cachexia biomarkers in patients with low-muscularity. The prognostic value of these biomarkers for predicting recurrence and survival outcome was confirmed using expression data from eight lung cancer datasets (validation set). Finally, C2C12 myoblasts differentiated into myotubes were used to evaluate the ability of the selected biomarker, interleukin (IL)-8, in inducing muscle cell atrophy. We identified 75 over-expressed transcripts in patients with low-muscularity, which included IL-6, CSF3, and IL-8. Also, we identified NCAM1, CNTN1, SCG2, CADM1, IL-8, NPTX1, and APOD as PSCB in the tumor secretome. These PSCB were capable of distinguishing worse and better prognosis (recurrence and survival) in NSCLC patients. IL-8 was confirmed as a predictor of worse prognosis in all validation sets. In vitro assays revealed that IL-8 promoted C2C12 myotube atrophy. Tumors from low-muscularity patients presented a set of upregulated genes encoding for secreted proteins, including pro-inflammatory cytokines that predict worse overall survival in NSCLC. Among these upregulated genes, IL-8 expression in NSCLC tissues was associated with worse prognosis, and the recombinant IL-8 was capable of triggering atrophy in C2C12 myotubes.

Algorithmic three-dimensional analysis of tumor shape in MRI improves prognosis of survival in glioblastoma: a multi-institutional study

  • Czarnek, Nicholas
  • Clark, Kal
  • Peters, Katherine B
  • Mazurowski, Maciej A
Journal of Neuro-Oncology 2017 Journal Article, cited 15 times
Website
In this retrospective, IRB-exempt study, we analyzed data from 68 patients diagnosed with glioblastoma (GBM) in two institutions and investigated the relationship between tumor shape, quantified using algorithmic analysis of magnetic resonance images, and survival. Each patient's Fluid Attenuated Inversion Recovery (FLAIR) abnormality and enhancing tumor were manually delineated, and tumor shape was analyzed by automatic computer algorithms. Five features were automatically extracted from the images to quantify the extent of irregularity in tumor shape in two and three dimensions. Univariate Cox proportional hazard regression analysis was performed to determine how prognostic each feature was of survival. Kaplan Meier analysis was performed to illustrate the prognostic value of each feature. To determine whether the proposed quantitative shape features have additional prognostic value compared with standard clinical features, we controlled for tumor volume, patient age, and Karnofsky Performance Score (KPS). The FLAIR-based bounding ellipsoid volume ratio (BEVR), a 3D complexity measure, was strongly prognostic of survival, with a hazard ratio of 0.36 (95% CI 0.20-0.65), and remained significant in regression analysis after controlling for other clinical factors (P = 0.0061). Three enhancing-tumor based shape features were prognostic of survival independently of clinical factors: BEVR (P = 0.0008), margin fluctuation (P = 0.0013), and angular standard deviation (P = 0.0078). Algorithmically assessed tumor shape is statistically significantly prognostic of survival for patients with GBM independently of patient age, KPS, and tumor volume. This shows promise for extending the utility of MR imaging in treatment of GBM patients.

Radiogenomics of glioblastoma: a pilot multi-institutional study to investigate a relationship between tumor shape features and tumor molecular subtype

  • Czarnek, Nicholas M
  • Clark, Kal
  • Peters, Katherine B
  • Collins, Leslie M
  • Mazurowski, Maciej A
2016 Conference Proceedings, cited 3 times
Website

Superpixel-based deep convolutional neural networks and active contour model for automatic prostate segmentation on 3D MRI scans

  • da Silva, Giovanni L F
  • Diniz, Petterson S
  • Ferreira, Jonnison L
  • Franca, Joao V F
  • Silva, Aristofanes C
  • de Paiva, Anselmo C
  • de Cavalcanti, Elton A A
2020 Journal Article, cited 0 times
Website
Automatic and reliable prostate segmentation is an essential prerequisite for assisting the diagnosis and treatment, such as guiding biopsy procedure and radiation therapy. Nonetheless, automatic segmentation is challenging due to the lack of clear prostate boundaries owing to the similar appearance of prostate and surrounding tissues and the wide variation in size and shape among different patients ascribed to pathological changes or different resolutions of images. In this regard, the state-of-the-art includes methods based on a probabilistic atlas, active contour models, and deep learning techniques. However, these techniques have limitations that need to be addressed, such as MRI scans with the same spatial resolution, initialization of the prostate region with well-defined contours and a set of hyperparameters of deep learning techniques determined manually, respectively. Therefore, this paper proposes an automatic and novel coarse-to-fine segmentation method for prostate 3D MRI scans. The coarse segmentation step combines local texture and spatial information using the Intrinsic Manifold Simple Linear Iterative Clustering algorithm and probabilistic atlas in a deep convolutional neural networks model jointly with the particle swarm optimization algorithm to classify prostate and non-prostate tissues. Then, the fine segmentation uses the 3D Chan-Vese active contour model to obtain the final prostate surface. The proposed method has been evaluated on the Prostate 3T and PROMISE12 databases presenting a dice similarity coefficient of 84.86%, relative volume difference of 14.53%, sensitivity of 90.73%, specificity of 99.46%, and accuracy of 99.11%. Experimental results demonstrate the high performance potential of the proposed method compared to those previously published.

Development of a Convolutional Neural Network Based Skull Segmentation in MRI Using Standard Tesselation Language Models

  • Dalvit Carvalho da Silva, Rodrigo
  • Jenkyn, Thomas Richard
  • Carranza, Victor Alexander
Journal of Personalized Medicine 2021 Journal Article, cited 0 times
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Development of a Convolutional Neural Network Based Skull Segmentation in MRI Using Standard Tesselation Language Models

  • Dalvit Carvalho da Silva, R.
  • Jenkyn, T. R.
  • Carranza, V. A.
J Pers Med 2021 Journal Article, cited 0 times
Website
Segmentation is crucial in medical imaging analysis to help extract regions of interest (ROI) from different imaging modalities. The aim of this study is to develop and train a 3D convolutional neural network (CNN) for skull segmentation in magnetic resonance imaging (MRI). 58 gold standard volumetric labels were created from computed tomography (CT) scans in standard tessellation language (STL) models. These STL models were converted into matrices and overlapped on the 58 corresponding MR images to create the MRI gold standards labels. The CNN was trained with these 58 MR images and a mean +/- standard deviation (SD) Dice similarity coefficient (DSC) of 0.7300 +/- 0.04 was achieved. A further investigation was carried out where the brain region was removed from the image with the help of a 3D CNN and manual corrections by using only MR images. This new dataset, without the brain, was presented to the previous CNN which reached a new mean +/- SD DSC of 0.7826 +/- 0.03. This paper aims to provide a framework for segmenting the skull using CNN and STL models, as the 3D CNN was able to segment the skull with a certain precision.

Immunotherapy in Metastatic Colorectal Cancer: Could the Latest Developments Hold the Key to Improving Patient Survival?

  • Damilakis, E.
  • Mavroudis, D.
  • Sfakianaki, M.
  • Souglakos, J.
Cancers (Basel) 2020 Journal Article, cited 0 times
Website
Immunotherapy has considerably increased the number of anticancer agents in many tumor types including metastatic colorectal cancer (mCRC). Anti-PD-1 (programmed death 1) and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) immune checkpoint inhibitors (ICI) have been shown to benefit the mCRC patients with mismatch repair deficiency (dMMR) or high microsatellite instability (MSI-H). However, ICI is not effective in mismatch repair proficient (pMMR) colorectal tumors, which constitute a large population of patients. Several clinical trials evaluating the efficacy of immunotherapy combined with chemotherapy, radiation therapy, or other agents are currently ongoing to extend the benefit of immunotherapy to pMMR mCRC cases. In dMMR patients, MSI testing through immunohistochemistry and/or polymerase chain reaction can be used to identify patients that will benefit from immunotherapy. Next-generation sequencing has the ability to detect MSI-H using a low amount of nucleic acids and its application in clinical practice is currently being explored. Preliminary data suggest that radiomics is capable of discriminating MSI from microsatellite stable mCRC and may play a role as an imaging biomarker in the future. Tumor mutational burden, neoantigen burden, tumor-infiltrating lymphocytes, immunoscore, and gastrointestinal microbiome are promising biomarkers that require further investigation and validation.

Feature Extraction In Medical Images by Using Deep Learning Approach

  • Dara, S
  • Tumma, P
  • Eluri, NR
  • Kancharla, GR
International Journal of Pure and Applied Mathematics 2018 Journal Article, cited 0 times
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AI-based Prognostic Imaging Biomarkers for Precision Neurooncology: the ReSPOND Consortium

  • Davatzikos, C.
  • Barnholtz-Sloan, J. S.
  • Bakas, S.
  • Colen, R.
  • Mahajan, A.
  • Quintero, C. B.
  • Font, J. C.
  • Puig, J.
  • Jain, R.
  • Sloan, A. E.
  • Badve, C.
  • Marcus, D. S.
  • Choi, Y. S.
  • Lee, S. K.
  • Chang, J. H.
  • Poisson, L. M.
  • Griffith, B.
  • Dicker, A. P.
  • Flanders, A. E.
  • Booth, T. C.
  • Rathore, S.
  • Akbari, H.
  • Sako, C.
  • Bilello, M.
  • Shukla, G.
  • Kazerooni, A. F.
  • Brem, S.
  • Lustig, R.
  • Mohan, S.
  • Bagley, S.
  • Nasrallah, M.
  • O'Rourke, D. M.
2020 Journal Article, cited 0 times
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Machine learning: a useful radiological adjunct in determination of a newly diagnosed glioma’s grade and IDH status

  • De Looze, Céline
  • Beausang, Alan
  • Cryan, Jane
  • Loftus, Teresa
  • Buckley, Patrick G
  • Farrell, Michael
  • Looby, Seamus
  • Reilly, Richard
  • Brett, Francesca
  • Kearney, Hugh
Journal of Neuro-Oncology 2018 Journal Article, cited 0 times

Local mesh ternary patterns: a new descriptor for MRI and CT biomedical image indexing and retrieval

  • Deep, G
  • Kaur, L
  • Gupta, S
Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization 2016 Journal Article, cited 3 times
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Directional local ternary quantized extrema pattern: A new descriptor for biomedical image indexing and retrieval

  • Deep, G
  • Kaur, L
  • Gupta, S
Engineering Science and Technology, an International Journal 2016 Journal Article, cited 9 times
Website

Predicting response before initiation of neoadjuvant chemotherapy in breast cancer using new methods for the analysis of dynamic contrast enhanced MRI (DCE MRI) data

  • DeGrandchamp, Joseph B
  • Whisenant, Jennifer G
  • Arlinghaus, Lori R
  • Abramson, VG
  • Yankeelov, Thomas E
  • Cárdenas-Rodríguez, Julio
2016 Conference Proceedings, cited 5 times
Website

Mesoscopic imaging of glioblastomas: Are diffusion, perfusion and spectroscopic measures influenced by the radiogenetic phenotype?

  • Demerath, Theo
  • Simon-Gabriel, Carl Philipp
  • Kellner, Elias
  • Schwarzwald, Ralf
  • Lange, Thomas
  • Heiland, Dieter Henrik
  • Reinacher, Peter
  • Staszewski, Ori
  • Mast, Hansjorg
  • Kiselev, Valerij G
  • Egger, Karl
  • Urbach, Horst
  • Weyerbrock, Astrid
  • Mader, Irina
Neuroradiology Journal 2017 Journal Article, cited 5 times
Website
The purpose of this study was to identify markers from perfusion, diffusion, and chemical shift imaging in glioblastomas (GBMs) and to correlate them with genetically determined and previously published patterns of structural magnetic resonance (MR) imaging. Twenty-six patients (mean age 60 years, 13 female) with GBM were investigated. Imaging consisted of native and contrast-enhanced 3D data, perfusion, diffusion, and spectroscopic imaging. In the presence of minor necrosis, cerebral blood volume (CBV) was higher (median +/- SD, 2.23% +/- 0.93) than in pronounced necrosis (1.02% +/- 0.71), pcorr = 0.0003. CBV adjacent to peritumoral fluid-attenuated inversion recovery (FLAIR) hyperintensity was lower in edema (1.72% +/- 0.31) than in infiltration (1.91% +/- 0.35), pcorr = 0.039. Axial diffusivity adjacent to peritumoral FLAIR hyperintensity was lower in severe mass effect (1.08*10(-3) mm(2)/s +/- 0.08) than in mild mass effect (1.14*10(-3) mm(2)/s +/- 0.06), pcorr = 0.048. Myo-inositol was positively correlated with a marker for mitosis (Ki-67) in contrast-enhancing tumor, r = 0.5, pcorr = 0.0002. Changed CBV and axial diffusivity, even outside FLAIR hyperintensity, in adjacent normal-appearing matter can be discussed as to be related to angiogenesis pathways and to activated proliferation genes. The correlation between myo-inositol and Ki-67 might be attributed to its binding to cell surface receptors regulating tumorous proliferation of astrocytic cells.

Computer-aided detection of lung nodules using outer surface features

  • Demir, Önder
  • Yılmaz Çamurcu, Ali
Bio-Medical Materials and EngineeringBio-Med Mater Eng 2015 Journal Article, cited 28 times
Website
In this study, a computer-aided detection (CAD) system was developed for the detection of lung nodules in computed tomography images. The CAD system consists of four phases, including two-dimensional and three-dimensional preprocessing phases. In the feature extraction phase, four different groups of features are extracted from volume of interests: morphological features, statistical and histogram features, statistical and histogram features of outer surface, and texture features of outer surface. The support vector machine algorithm is optimized using particle swarm optimization for classification. The CAD system provides 97.37% sensitivity, 86.38% selectivity, 88.97% accuracy and 2.7 false positive per scan using three groups of classification features. After the inclusion of outer surface texture features, classification results of the CAD system reaches 98.03% sensitivity, 87.71% selectivity, 90.12% accuracy and 2.45 false positive per scan. Experimental results demonstrate that outer surface texture features of nodule candidates are useful to increase sensitivity and decrease the number of false positives in the detection of lung nodules in computed tomography images.

Investigation of inter-fraction target motion variations in the context of pencil beam scanned proton therapy in non-small cell lung cancer patients

  • den Otter, L. A.
  • Anakotta, R. M.
  • Weessies, M.
  • Roos, C. T. G.
  • Sijtsema, N. M.
  • Muijs, C. T.
  • Dieters, M.
  • Wijsman, R.
  • Troost, E. G. C.
  • Richter, C.
  • Meijers, A.
  • Langendijk, J. A.
  • Both, S.
  • Knopf, A. C.
Med Phys 2020 Journal Article, cited 0 times
Website
PURPOSE: For locally advanced-stage non-small cell lung cancer (NSCLC), inter-fraction target motion variations during the whole time span of a fractionated treatment course are assessed in a large and representative patient cohort. The primary objective is to develop a suitable motion monitoring strategy for pencil beam scanning proton therapy (PBS-PT) treatments of NSCLC patients during free breathing. METHODS: Weekly 4D computed tomography (4DCT; 41 patients) and daily 4D cone beam computed tomography (4DCBCT; 10 of 41 patients) scans were analyzed for a fully fractionated treatment course. Gross tumor volumes (GTVs) were contoured and the 3D displacement vectors of the centroid positions were compared for all scans. Furthermore, motion amplitude variations in different lung segments were statistically analyzed. The dosimetric impact of target motion variations and target motion assessment was investigated in exemplary patient cases. RESULTS: The median observed centroid motion was 3.4 mm (range: 0.2-12.4 mm) with an average variation of 2.2 mm (range: 0.1-8.8 mm). Ten of 32 patients (31.3%) with an initial motion <5 mm increased beyond a 5-mm motion amplitude during the treatment course. Motion observed in the 4DCBCT scans deviated on average 1.5 mm (range: 0.0-6.0 mm) from the motion observed in the 4DCTs. Larger motion variations for one example patient compromised treatment plan robustness while no dosimetric influence was seen due to motion assessment biases in another example case. CONCLUSIONS: Target motion variations were investigated during the course of radiotherapy for NSCLC patients. Patients with initial GTV motion amplitudes of < 2 mm can be assumed to be stable in motion during the treatment course. For treatments of NSCLC patients who exhibit motion amplitudes of > 2 mm, 4DCBCT should be considered for motion monitoring due to substantial motion variations observed.

Development of a nomogram combining clinical staging with 18F-FDG PET/CT image features in non-small-cell lung cancer stage I–III

  • Desseroit, Marie-Charlotte
  • Visvikis, Dimitris
  • Tixier, Florent
  • Majdoub, Mohamed
  • Perdrisot, Rémy
  • Guillevin, Rémy
  • Le Rest, Catherine Cheze
  • Hatt, Mathieu
European journal of nuclear medicine and molecular imaging 2016 Journal Article, cited 34 times
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Spatial habitats from multiparametric MR imaging are associated with signaling pathway activities and survival in glioblastoma

  • Dextraze, Katherine
  • Saha, Abhijoy
  • Kim, Donnie
  • Narang, Shivali
  • Lehrer, Michael
  • Rao, Anita
  • Narang, Saphal
  • Rao, Dinesh
  • Ahmed, Salmaan
  • Madhugiri, Venkatesh
  • Fuller, Clifton David
  • Kim, Michelle M
  • Krishnan, Sunil
  • Rao, Ganesh
  • Rao, Arvind
OncotargetOncotarget 2017 Journal Article, cited 0 times
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Glioblastoma (GBM) show significant inter- and intra-tumoral heterogeneity, impacting response to treatment and overall survival time of 12-15 months. To study glioblastoma phenotypic heterogeneity, multi-parametric magnetic resonance images (MRI) of 85 glioblastoma patients from The Cancer Genome Atlas were analyzed to characterize tumor-derived spatial habitats for their relationship with outcome (overall survival) and to identify their molecular correlates (i.e., determine associated tumor signaling pathways correlated with imaging-derived habitat measurements). Tumor sub-regions based on four sequences (fluid attenuated inversion recovery, T1-weighted, post-contrast T1-weighted, and T2-weighted) were defined by automated segmentation. From relative intensity of pixels in the 3-dimensional tumor region, "imaging habitats" were identified and analyzed for their association to clinical and genetic data using survival modeling and Dirichlet regression, respectively. Sixteen distinct tumor sub-regions ("spatial imaging habitats") were derived, and those associated with overall survival (denoted "relevant" habitats) in glioblastoma patients were identified. Dirichlet regression implicated each relevant habitat with unique pathway alterations. Relevant habitats also had some pathways and cellular processes in common, including phosphorylation of STAT-1 and natural killer cell activity, consistent with cancer hallmarks. This work revealed clinical relevance of MRI-derived spatial habitats and their relationship with oncogenic molecular mechanisms in patients with GBM. Characterizing the associations between imaging-derived phenotypic measurements with the genomic and molecular characteristics of tumors can enable insights into tumor biology, further enabling the practice of personalized cancer treatment. The analytical framework and workflow demonstrated in this study are inherently scalable to multiple MR sequences.

Measurement of spiculation index in 3D for solitary pulmonary nodules in volumetric lung CT images

  • Dhara, Ashis Kumar
  • Mukhopadhyay, Sudipta
  • Alam, Naved
  • Khandelwal, Niranjan
2013 Conference Paper, cited 4 times
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3d texture analysis of solitary pulmonary nodules using co-occurrence matrix from volumetric lung CT images

  • Dhara, Ashis Kumar
  • Mukhopadhyay, Sudipta
  • Khandelwal, Niranjan
2013 Conference Proceedings, cited 7 times
Website

Deep learning in head & neck cancer outcome prediction

  • Diamant, André
  • Chatterjee, Avishek
  • Vallières, Martin
  • Shenouda, George
  • Seuntjens, Jan
2019 Journal Article, cited 0 times
Website
Traditional radiomics involves the extraction of quantitative texture features from medical images in an attempt to determine correlations with clinical endpoints. We hypothesize that convolutional neural networks (CNNs) could enhance the performance of traditional radiomics, by detecting image patterns that may not be covered by a traditional radiomic framework. We test this hypothesis by training a CNN to predict treatment outcomes of patients with head and neck squamous cell carcinoma, based solely on their pre-treatment computed tomography image. The training (194 patients) and validation sets (106 patients), which are mutually independent and include 4 institutions, come from The Cancer Imaging Archive. When compared to a traditional radiomic framework applied to the same patient cohort, our method results in a AUC of 0.88 in predicting distant metastasis. When combining our model with the previous model, the AUC improves to 0.92. Our framework yields models that are shown to explicitly recognize traditional radiomic features, be directly visualized and perform accurate outcome prediction.

Human-interpretable image features derived from densely mapped cancer pathology slides predict diverse molecular phenotypes

  • Diao, J. A.
  • Wang, J. K.
  • Chui, W. F.
  • Mountain, V.
  • Gullapally, S. C.
  • Srinivasan, R.
  • Mitchell, R. N.
  • Glass, B.
  • Hoffman, S.
  • Rao, S. K.
  • Maheshwari, C.
  • Lahiri, A.
  • Prakash, A.
  • McLoughlin, R.
  • Kerner, J. K.
  • Resnick, M. B.
  • Montalto, M. C.
  • Khosla, A.
  • Wapinski, I. N.
  • Beck, A. H.
  • Elliott, H. L.
  • Taylor-Weiner, A.
2021 Journal Article, cited 0 times
Website
Computational methods have made substantial progress in improving the accuracy and throughput of pathology workflows for diagnostic, prognostic, and genomic prediction. Still, lack of interpretability remains a significant barrier to clinical integration. We present an approach for predicting clinically-relevant molecular phenotypes from whole-slide histopathology images using human-interpretable image features (HIFs). Our method leverages >1.6 million annotations from board-certified pathologists across >5700 samples to train deep learning models for cell and tissue classification that can exhaustively map whole-slide images at two and four micron-resolution. Cell- and tissue-type model outputs are combined into 607 HIFs that quantify specific and biologically-relevant characteristics across five cancer types. We demonstrate that these HIFs correlate with well-known markers of the tumor microenvironment and can predict diverse molecular signatures (AUROC 0.601-0.864), including expression of four immune checkpoint proteins and homologous recombination deficiency, with performance comparable to 'black-box' methods. Our HIF-based approach provides a comprehensive, quantitative, and interpretable window into the composition and spatial architecture of the tumor microenvironment.

Theoretical tumor edge detection technique using multiple Bragg peak decomposition in carbon ion therapy

  • Dias, Marta Filipa Ferraz
  • Collins-Fekete, Charles-Antoine
  • Baroni, Guido
  • Riboldi, Marco
  • Seco, Joao
Biomedical Physics & Engineering Express 2019 Journal Article, cited 0 times
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Automated segmentation refinement of small lung nodules in CT scans by local shape analysis

  • Diciotti, Stefano
  • Lombardo, Simone
  • Falchini, Massimo
  • Picozzi, Giulia
  • Mascalchi, Mario
IEEE Trans Biomed Eng 2011 Journal Article, cited 68 times
Website
One of the most important problems in the segmentation of lung nodules in CT imaging arises from possible attachments occurring between nodules and other lung structures, such as vessels or pleura. In this report, we address the problem of vessels attachments by proposing an automated correction method applied to an initial rough segmentation of the lung nodule. The method is based on a local shape analysis of the initial segmentation making use of 3-D geodesic distance map representations. The correction method has the advantage that it locally refines the nodule segmentation along recognized vessel attachments only, without modifying the nodule boundary elsewhere. The method was tested using a simple initial rough segmentation, obtained by a fixed image thresholding. The validation of the complete segmentation algorithm was carried out on small lung nodules, identified in the ITALUNG screening trial and on small nodules of the lung image database consortium (LIDC) dataset. In fully automated mode, 217/256 (84.8%) lung nodules of ITALUNG and 139/157 (88.5%) individual marks of lung nodules of LIDC were correctly outlined and an excellent reproducibility was also observed. By using an additional interactive mode, based on a controlled manual interaction, 233/256 (91.0%) lung nodules of ITALUNG and 144/157 (91.7%) individual marks of lung nodules of LIDC were overall correctly segmented. The proposed correction method could also be usefully applied to any existent nodule segmentation algorithm for improving the segmentation quality of juxta-vascular nodules.

Feature-Enhanced Graph Networks for Genetic Mutational Prediction Using Histopathological Images in Colon Cancer

  • Ding, Kexin
  • Liu, Qiao
  • Lee, Edward
  • Zhou, Mu
  • Lu, Aidong
  • Zhang, Shaoting
2020 Conference Proceedings, cited 0 times
Website
Mining histopathological and genetic data provides a unique avenue to deepen our understanding of cancer biology. However, extensive cancer heterogeneity across image- and molecular-scales poses technical challenges for feature extraction and outcome prediction. In this study, we propose a feature-enhanced graph network (FENet) for genetic mutation prediction using histopathological images in colon cancer. Unlike conventional approaches analyzing patch-based feature alone without considering their spatial connectivity, we seek to link and explore non-isomorphic topological structures in histopathological images. Our FENet incorporates feature enhancement in convolutional graph neural networks to aggregate discriminative features for capturing gene mutation status. Specifically, our approach could identify both local patch feature information and global topological structure in histopathological images simultaneously. Furthermore, we introduced an ensemble strategy by constructing multiple subgraphs to boost the prediction performance. Extensive experiments on the TCGA-COAD and TCGA-READ cohort including both histopathological images and three key genes’ mutation profiles (APC, KRAS, and TP53) demonstrated the superiority of FENet for key mutational outcome prediction in colon cancer.

Breast Cancer Mass Detection in Mammograms Using Gray Difference Weight and MSER Detector

  • Divyashree, B. V.
  • Kumar, G. Hemantha
SN Computer Science 2021 Journal Article, cited 0 times
Website
Breast cancer is a deadly and one of the most prevalent cancers in women across the globe. Mammography is widely used imaging modality for diagnosis and screening of breast cancer. Segmentation of breast region and mass detection are crucial steps in automatic breast cancer detection. Due to the non-uniform distribution of various tissues, it is a challenging task to analyze mammographic images with high accuracy. In this paper, background suppression and pectoral muscle removal are performed using gradient weight map followed by gray difference weight and fast marching method. Enhancement of breast region is performed using contrast limited adaptive histogram equalization (CLAHE) and de-correlation stretch. Detection of breast masses is accomplished by gray difference weight and maximally stable external regions (MSER) detector. Experimentation on Mammographic Image Analysis Society (MIAS) and curated breast imaging subset of digital database for screening mammography (CBIS-DDSM) show that the method proposed performs breast boundary segmentation and mass detection with best accuracies. Mass detection achieved high accuracies of about 97.64% and 94.66% for MIAS and CBIS-DDSM dataset, respectively. The method is simple, robust, less affected to noise, density, shape and size which could provide reasonable support for mammographic analysis.

An introduction to Topological Object Data Analysis

  • Dixon, Adam
  • Patrangenaru, Victor
  • Shen, Chen
2020 Conference Proceedings, cited 1 times
Website
Summary and analysis are important foundations in Statistics, but typical methods may prove ineffective at providing thorough summaries of complex object data. Topological data analysis (TDA) (also called topological object data analysis (TODA) when applied to object data) provides additional topological summaries, such as the persistence diagram and persistence landscape, that can be useful in distinguishing distributions based on data sets. The main tool is persistent homology, which tracks the births and deaths of various homology classes as one steps through a filtered simplicial complex that covers the sample. The persistence diagrams and landscapes can also be used to provide confidence sets for “significant” features and two-sample tests between groups. An example of application is provided via analyzing mammogram images for patients with benign and malignant masses.

Learning Multi-Class Segmentations From Single-Class Datasets

  • Dmitriev, Konstantin
  • Kaufman, Arie
2019 Conference Paper, cited 1 times
Website
Multi-class segmentation has recently achieved significant performance in natural images and videos. This achievement is due primarily to the public availability of large multi-class datasets. However, there are certain domains, such as biomedical images, where obtaining sufficient multi-class annotations is a laborious and often impossible task and only single-class datasets are available. While existing segmentation research in such domains use private multi-class datasets or focus on single-class segmentations, we propose a unified highly efficient framework for robust simultaneous learning of multi-class segmentations by combining single-class datasets and utilizing a novel way of conditioning a convolutional network for the purpose of segmentation. We demonstrate various ways of incorporating the conditional information, perform an extensive evaluation, and show compelling multi-class segmentation performance on biomedical images, which outperforms current state-of-the-art solutions (up to 2.7%). Unlike current solutions, which are meticulously tailored for particular single-class datasets, we utilize datasets from a variety of sources. Furthermore, we show the applicability of our method also to natural images and evaluate it on the Cityscapes dataset. We further discuss other possible applications of our proposed framework.

Assessment of Renal Cell Carcinoma by Texture Analysis in Clinical Practice: A Six-Site, Six-Platform Analysis of Reliability

  • Doshi, A. M.
  • Tong, A.
  • Davenport, M. S.
  • Khalaf, A.
  • Mresh, R.
  • Rusinek, H.
  • Schieda, N.
  • Shinagare, A.
  • Smith, A. D.
  • Thornhill, R.
  • Vikram, R.
  • Chandarana, H.
AJR Am J Roentgenol 2021 Journal Article, cited 0 times
Website
Background: Multiple commercial and open-source software applications are available for texture analysis. Nonstandard techniques can cause undesirable variability that impedes result reproducibility and limits clinical utility. Objective: The purpose of this study is to measure agreement of texture metrics extracted by 6 software packages. Methods: This retrospective study included 40 renal cell carcinomas with contrast-enhanced CT from The Cancer Genome Atlas and Imaging Archive. Images were analyzed by 7 readers at 6 sites. Each reader used 1 of 6 software packages to extract commonly studied texture features. Inter and intra-reader agreement for segmentation was assessed with intra-class correlation coefficients. First-order (available in 6 packages) and second-order (available in 3 packages) texture features were compared between software pairs using Pearson correlation. Results: Inter- and intra-reader agreement was excellent (ICC 0.93-1). First-order feature correlations were strong (r>0.8, p<0.001) between 75% (21/28) of software pairs for mean and standard deviation, 48% (10/21) for entropy, 29% (8/28) for skewness, and 25% (7/28) for kurtosis. Of 15 second-order features, only co-occurrence matrix correlation, grey-level non-uniformity, and run-length non-uniformity showed strong correlation between software packages (0.90-1, p<0.001). Conclusion: Variability in first and second order texture features was common across software configurations and produced inconsistent results. Standardized algorithms and reporting methods are needed before texture data can be reliably used for clinical applications. Clinical Impact: It is important to be aware of variability related to texture software processing and configuration when reporting and comparing outputs.

Long short-term memory networks predict breast cancer recurrence in analysis of consecutive MRIs acquired during the course of neoadjuvant chemotherapy

  • Drukker, Karen
  • Edwards, Alexandra
  • Papaioannou, John
  • Giger, Maryellen
  • Hahn, Horst K.
  • Mazurowski, Maciej A.
2020 Conference Paper, cited 0 times
Website
The purpose of this study was to assess long short-term memory networks in the prediction of recurrence-free survival in breast cancer patients using features extracted from MRIs acquired during the course of neoadjuvant chemotherapy. In the I-SPY1 dataset, up to 4 MRI exams were available per patient acquired at pre-treatment, early-treatment, interregimen, and pre-surgery time points. Breast cancers were automatically segmented and 8 features describing kinetic curve characteristics were extracted. We assessed performance of long short-term memory networks in the prediction of recurrence-free survival status at 2 years and at 5 years post-surgery. For these predictions, we analyzed MRIs from women who had at least 2 (or 5) years of recurrence-free follow-up or experienced recurrence or death within that timeframe: 157 women and 73 women, respectively. One approach used features extracted from all available exams and the other approach used features extracted from only exams prior to the second cycle of neoadjuvant chemotherapy. The areas under the ROC curve in the prediction of recurrence-free survival status at 2 years post-surgery were 0.80, 95% confidence interval [0.68; 0.88] and 0.75 [0.62; 0.83] for networks trained with all 4 available exams and only the ‘early’ exams, respectively. Hazard ratios at the lowest, median, and highest quartile cut -points were 6.29 [2.91; 13.62], 3.27 [1.77; 6.03], 1.65 [0.83; 3.27] and 2.56 [1.20; 5.48], 3.01 [1.61; 5.66], 2.30 [1.14; 4.67]. Long short-term memory networks were able to predict recurrence-free survival in breast cancer patients, also when analyzing only MRIs acquired ‘early on’ during neoadjuvant treatment.

Most-enhancing tumor volume by MRI radiomics predicts recurrence-free survival “early on” in neoadjuvant treatment of breast cancer

  • Drukker, Karen
  • Li, Hui
  • Antropova, Natalia
  • Edwards, Alexandra
  • Papaioannou, John
  • Giger, Maryellen L
Cancer Imaging 2018 Journal Article, cited 0 times
Website
BACKGROUND: The hypothesis of this study was that MRI-based radiomics has the ability to predict recurrence-free survival "early on" in breast cancer neoadjuvant chemotherapy. METHODS: A subset, based on availability, of the ACRIN 6657 dynamic contrast-enhanced MR images was used in which we analyzed images of all women imaged at pre-treatment baseline (141 women: 40 with a recurrence, 101 without) and all those imaged after completion of the first cycle of chemotherapy, i.e., at early treatment (143 women: 37 with a recurrence vs. 105 without). Our method was completely automated apart from manual localization of the approximate tumor center. The most enhancing tumor volume (METV) was automatically calculated for the pre-treatment and early treatment exams. Performance of METV in the task of predicting a recurrence was evaluated using ROC analysis. The association of recurrence-free survival with METV was assessed using a Cox regression model controlling for patient age, race, and hormone receptor status and evaluated by C-statistics. Kaplan-Meier analysis was used to estimate survival functions. RESULTS: The C-statistics for the association of METV with recurrence-free survival were 0.69 with 95% confidence interval of [0.58; 0.80] at pre-treatment and 0.72 [0.60; 0.84] at early treatment. The hazard ratios calculated from Kaplan-Meier curves were 2.28 [1.08; 4.61], 3.43 [1.83; 6.75], and 4.81 [2.16; 10.72] for the lowest quartile, median quartile, and upper quartile cut-points for METV at early treatment, respectively. CONCLUSION: The performance of the automatically-calculated METV rivaled that of a semi-manual model described for the ACRIN 6657 study (published C-statistic 0.72 [0.60; 0.84]), which involved the same dataset but required semi-manual delineation of the functional tumor volume (FTV) and knowledge of the pre-surgical residual cancer burden.

Local Wavelet Pattern: A New Feature Descriptor for Image Retrieval in Medical CT Databases

  • Dubey, Shiv Ram
  • Singh, Satish Kumar
  • Singh, Rajat Kumar
IEEE Trans Image Process 2015 Journal Article, cited 52 times
Website
A new image feature description based on the local wavelet pattern (LWP) is proposed in this paper to characterize the medical computer tomography (CT) images for content-based CT image retrieval. In the proposed work, the LWP is derived for each pixel of the CT image by utilizing the relationship of center pixel with the local neighboring information. In contrast to the local binary pattern that only considers the relationship between a center pixel and its neighboring pixels, the presented approach first utilizes the relationship among the neighboring pixels using local wavelet decomposition, and finally considers its relationship with the center pixel. A center pixel transformation scheme is introduced to match the range of center value with the range of local wavelet decomposed values. Moreover, the introduced local wavelet decomposition scheme is centrally symmetric and suitable for CT images. The novelty of this paper lies in the following two ways: 1) encoding local neighboring information with local wavelet decomposition and 2) computing LWP using local wavelet decomposed values and transformed center pixel values. We tested the performance of our method over three CT image databases in terms of the precision and recall. We also compared the proposed LWP descriptor with the other state-of-the-art local image descriptors, and the experimental results suggest that the proposed method outperforms other methods for CT image retrieval.

An Ad Hoc Random Initialization Deep Neural Network Architecture for Discriminating Malignant Breast Cancer Lesions in Mammographic Images

  • Duggento, Andrea
  • Aiello, Marco
  • Cavaliere, Carlo
  • Cascella, Giuseppe L
  • Cascella, Davide
  • Conte, Giovanni
  • Guerrisi, Maria
  • Toschi, Nicola
Contrast Media Mol Imaging 2019 Journal Article, cited 1 times
Website
Breast cancer is one of the most common cancers in women, with more than 1,300,000 cases and 450,000 deaths each year worldwide. In this context, recent studies showed that early breast cancer detection, along with suitable treatment, could significantly reduce breast cancer death rates in the long term. X-ray mammography is still the instrument of choice in breast cancer screening. In this context, the false-positive and false-negative rates commonly achieved by radiologists are extremely arduous to estimate and control although some authors have estimated figures of up to 20% of total diagnoses or more. The introduction of novel artificial intelligence (AI) technologies applied to the diagnosis and, possibly, prognosis of breast cancer could revolutionize the current status of the management of the breast cancer patient by assisting the radiologist in clinical image interpretation. Lately, a breakthrough in the AI field has been brought about by the introduction of deep learning techniques in general and of convolutional neural networks in particular. Such techniques require no a priori feature space definition from the operator and are able to achieve classification performances which can even surpass human experts. In this paper, we design and validate an ad hoc CNN architecture specialized in breast lesion classification from imaging data only. We explore a total of 260 model architectures in a train-validation-test split in order to propose a model selection criterion which can pose the emphasis on reducing false negatives while still retaining acceptable accuracy. We achieve an area under the receiver operatic characteristics curve of 0.785 (accuracy 71.19%) on the test set, demonstrating how an ad hoc random initialization architecture can and should be fine tuned to a specific problem, especially in biomedical applications.

Assessing the Effects of Software Platforms on Volumetric Segmentation of Glioblastoma

  • Dunn, William D Jr
  • Aerts, Hugo J W L
  • Cooper, Lee A
  • Holder, Chad A
  • Hwang, Scott N
  • Jaffe, Carle C
  • Brat, Daniel J
  • Jain, Rajan
  • Flanders, Adam E
  • Zinn, Pascal O
  • Colen, Rivka R
  • Gutman, David A
J Neuroimaging Psychiatry Neurol 2016 Journal Article, cited 0 times
Website
Background: Radiological assessments of biologically relevant regions in glioblastoma have been associated with genotypic characteristics, implying a potential role in personalized medicine. Here, we assess the reproducibility and association with survival of two volumetric segmentation platforms and explore how methodology could impact subsequent interpretation and analysis. Methods: Post-contrast T1- and T2-weighted FLAIR MR images of 67 TCGA patients were segmented into five distinct compartments (necrosis, contrast-enhancement, FLAIR, post contrast abnormal, and total abnormal tumor volumes) by two quantitative image segmentation platforms - 3D Slicer and a method based on Velocity AI and FSL. We investigated the internal consistency of each platform by correlation statistics, association with survival, and concordance with consensus neuroradiologist ratings using ordinal logistic regression. Results: We found high correlations between the two platforms for FLAIR, post contrast abnormal, and total abnormal tumor volumes (spearman's r(67) = 0.952, 0.959, and 0.969 respectively). Only modest agreement was observed for necrosis and contrast-enhancement volumes (r(67) = 0.693 and 0.773 respectively), likely arising from differences in manual and automated segmentation methods of these regions by 3D Slicer and Velocity AI/FSL, respectively. Survival analysis based on AUC revealed significant predictive power of both platforms for the following volumes: contrast-enhancement, post contrast abnormal, and total abnormal tumor volumes. Finally, ordinal logistic regression demonstrated correspondence to manual ratings for several features. Conclusion: Tumor volume measurements from both volumetric platforms produced highly concordant and reproducible estimates across platforms for general features. As automated or semi-automated volumetric measurements replace manual linear or area measurements, it will become increasingly important to keep in mind that measurement differences between segmentation platforms for more detailed features could influence downstream survival or radio genomic analyses.

Improving Brain Tumor Diagnosis Using MRI Segmentation Based on Collaboration of Beta Mixture Model and Learning Automata

  • Edalati-rad, Akram
  • Mosleh, Mohammad
Arabian Journal for Science and Engineering 2018 Journal Article, cited 0 times
Website

Automated 3-D Tissue Segmentation Via Clustering

  • Edwards, Samuel
  • Brown, Scott
  • Lee, Michael
Journal of Biomedical Engineering and Medical Imaging 2018 Journal Article, cited 0 times

Performance Analysis of Prediction Methods for Lossless Image Compression

  • Egorov, Nickolay
  • Novikov, Dmitriy
  • Gilmutdinov, Marat
2015 Book Section, cited 4 times
Website

Decision forests for learning prostate cancer probability maps from multiparametric MRI

  • Ehrenberg, Henry R
  • Cornfeld, Daniel
  • Nawaf, Cayce B
  • Sprenkle, Preston C
  • Duncan, James S
2016 Conference Proceedings, cited 2 times
Website

A Content-Based-Image-Retrieval Approach for Medical Image Repositories

  • el Rifai, Diaa
  • Maeder, Anthony
  • Liyanage, Liwan
2015 Conference Paper, cited 2 times
Website

Feature Extraction and Analysis for Lung Nodule Classification using Random Forest

  • Nada El-Askary
  • Mohammed Salem
  • Mohammed Roushdy
2019 Conference Paper, cited 0 times
Website

Extraction of Cancer Section from 2D Breast MRI Slice Using Brain Strom Optimization

  • Elanthirayan, R
  • Kubra, K Sakeenathul
  • Rajinikanth, V
  • Raja, N Sri Madhava
  • Satapathy, Suresh Chandra
2021 Book Section, cited 0 times
Website

Imaging genomics of glioblastoma: state of the art bridge between genomics and neuroradiology

  • ElBanan, Mohamed G
  • Amer, Ahmed M
  • Zinn, Pascal O
  • Colen, Rivka R
2015 Journal Article, cited 29 times
Website
Glioblastoma (GBM) is the most common and most aggressive primary malignant tumor of the central nervous system. Recently, researchers concluded that the "one-size-fits-all" approach for treatment of GBM is no longer valid and research should be directed toward more personalized and patient-tailored treatment protocols. Identification of the molecular and genomic pathways underlying GBM is essential for achieving this personalized and targeted therapeutic approach. Imaging genomics represents a new era as a noninvasive surrogate for genomic and molecular profile identification. This article discusses the basics of imaging genomics of GBM, its role in treatment decision-making, and its future potential in noninvasive genomic identification.

The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research Database

  • Elbers, Danne C.
  • Fillmore, Nathanael R.
  • Sung, Feng-Chi
  • Ganas, Spyridon S.
  • Prokhorenkov, Andrew
  • Meyer, Christopher
  • Hall, Robert B.
  • Ajjarapu, Samuel J.
  • Chen, Daniel C.
  • Meng, Frank
  • Grossman, Robert L.
  • Brophy, Mary T.
  • Do, Nhan V.
Patterns 2020 Journal Article, cited 0 times
Website
The Veterans Affairs Precision Oncology Data Repository (VA-PODR) is a large, nationwide repository of de-identified data on patients diagnosed with cancer at the Department of Veterans Affairs (VA). Data include longitudinal clinical data from the VA's nationwide electronic health record system and the VA Central Cancer Registry, targeted tumor sequencing data, and medical imaging data including computed tomography (CT) scans and pathology slides. A subset of the repository is available at the Genomic Data Commons (GDC) and The Cancer Imaging Archive (TCIA), and the full repository is available through the Veterans Precision Oncology Data Commons (VPODC). By releasing this de-identified dataset, we aim to advance Veterans' health care through enabling translational research on the Veteran population by a wide variety of researchers.

A genome-wide gain-of-function screen identifies CDKN2C as a HBV host factor

  • Eller, Carla
  • Heydmann, Laura
  • Colpitts, Che C.
  • El Saghire, Houssein
  • Piccioni, Federica
  • Jühling, Frank
  • Majzoub, Karim
  • Pons, Caroline
  • Bach, Charlotte
  • Lucifora, Julie
  • Lupberger, Joachim
  • Nassal, Michael
  • Cowley, Glenn S.
  • Fujiwara, Naoto
  • Hsieh, Sen-Yung
  • Hoshida, Yujin
  • Felli, Emanuele
  • Pessaux, Patrick
  • Sureau, Camille
  • Schuster, Catherine
  • Root, David E.
  • Verrier, Eloi R.
  • Baumert, Thomas F.
Nature Communications 2020 Journal Article, cited 0 times
Website
Chronic HBV infection is a major cause of liver disease and cancer worldwide. Approaches for cure are lacking, and the knowledge of virus-host interactions is still limited. Here, we perform a genome-wide gain-of-function screen using a poorly permissive hepatoma cell line to uncover host factors enhancing HBV infection. Validation studies in primary human hepatocytes identified CDKN2C as an important host factor for HBV replication. CDKN2C is overexpressed in highly permissive cells and HBV-infected patients. Mechanistic studies show a role for CDKN2C in inducing cell cycle G1 arrest through inhibition of CDK4/6 associated with the upregulation of HBV transcription enhancers. A correlation between CDKN2C expression and disease progression in HBV-infected patients suggests a role in HBV-induced liver disease. Taken together, we identify a previously undiscovered clinically relevant HBV host factor, allowing the development of improved infectious model systems for drug discovery and the study of the HBV life cycle.

Diffusion MRI quality control and functional diffusion map results in ACRIN 6677/RTOG 0625: a multicenter, randomized, phase II trial of bevacizumab and chemotherapy in recurrent glioblastoma

  • Ellingson, Benjamin M
  • Kim, Eunhee
  • Woodworth, Davis C
  • Marques, Helga
  • Boxerman, Jerrold L
  • Safriel, Yair
  • McKinstry, Robert C
  • Bokstein, Felix
  • Jain, Rajan
  • Chi, T Linda
  • Sorensen, A Gregory
  • Gilbert, Mark R
  • Barboriak, Daniel P
Int J Oncol 2015 Journal Article, cited 27 times
Website
Functional diffusion mapping (fDM) is a cancer imaging technique that quantifies voxelwise changes in apparent diffusion coefficient (ADC). Previous studies have shown value of fDMs in bevacizumab therapy for recurrent glioblastoma multiforme (GBM). The aim of the present study was to implement explicit criteria for diffusion MRI quality control and independently evaluate fDM performance in a multicenter clinical trial (RTOG 0625/ACRIN 6677). A total of 123 patients were enrolled in the current multicenter trial and signed institutional review board-approved informed consent at their respective institutions. MRI was acquired prior to and 8 weeks following therapy. A 5-point QC scoring system was used to evaluate DWI quality. fDM performance was evaluated according to the correlation of these metrics with PFS and OS at the first follow-up time-point. Results showed ADC variability of 7.3% in NAWM and 10.5% in CSF. A total of 68% of patients had usable DWI data and 47% of patients had high quality DWI data when also excluding patients that progressed before the first follow-up. fDM performance was improved by using only the highest quality DWI. High pre-treatment contrast enhancing tumor volume was associated with shorter PFS and OS. A high volume fraction of increasing ADC after therapy was associated with shorter PFS, while a high volume fraction of decreasing ADC was associated with shorter OS. In summary, DWI in multicenter trials are currently of limited value due to image quality. Improvements in consistency of image quality in multicenter trials are necessary for further advancement of DWI biomarkers.

A Novel Hybrid Perceptron Neural Network Algorithm for Classifying Breast MRI Tumors

  • ElNawasany, Amal M
  • Ali, Ahmed Fouad
  • Waheed, Mohamed E
2014 Book Section, cited 3 times
Website
Breast cancer today is the leading cause of death amongstcancer patients inflicting women around the world. Breast cancer is themost common cancer in women worldwide. It is also the principle cause ofdeath from cancer among women globally. Early detection of this diseasecan greatly enhance the chances of long-term survival of breast cancervictims. Classification of cancer data helps widely in detection of the dis-ease and it can be achieved using many techniques such as Perceptronwhich is an Artificial Neural Network (ANN) classification technique.In this paper, we proposed a new hybrid algorithm by combining theperceptron algorithm and the feature extraction algorithm after apply-ing the Scale Invariant Feature Transform (SIFT) algorithm in orderto classify magnetic resonance imaging (MRI) breast cancer images. Theproposed algorithm is called breast MRI cancer classifier (BMRICC) andit has been tested tested on 281 MRI breast images (138 abnormal and143 normal). The numerical results of the general performance of theBMRICC algorithm and the comparasion results between it and other 5benchmark classifiers show that, the BMRICC algorithm is a promisingalgorithm and its performance is better than the other algorithms.

A COMPUTER AIDED DIAGNOSIS SYSTEM FOR LUNG CANCER DETECTION USING SVM

  • EMİRZADE, ERKAN
2016 Thesis, cited 1 times
Website
Computer aided diagnosis is starting to be implemented broadly in the diagnosis and detection of many varieties of abnormities acquired during various imaging procedures. The main aim of the CAD systems is to increase the accuracy and decrease the time of diagnoses, while the general achievement for CAD systems are to find the place of nodules and to determine the characteristic features of the nodule. As lung cancer is one of the fatal and leading cancer types, there has been plenty of studies for the usage of the CAD systems to detect lung cancer. Yet, the CAD systems need to be developed a lot in order to identify the different shapes of nodules, lung segmentation and to have higher level of sensitivity, specifity and accuracy. This challenge is the motivation of this study in implementation of CAD system for lung cancer detection. In the study, LIDC database is used which comprises of an image set of lung cancer thoracic documented CT scans. The presented CAD system consists of CT image reading, image pre-processing, segmentation, feature extraction and classification steps. To avoid losing important features, the CT images were read as a raw form in DICOM file format. Then, filtration and enhancement techniques were used as an image processing. Otsu’s algorithm, edge detection and morphological operations are applied for the segmentation, following the feature extractions step. Finally, support vector machine with Gaussian RBF is utilized for the classification step which is widely used as a supervised classifier.

4D robust optimization including uncertainties in time structures can reduce the interplay effect in proton pencil beam scanning radiation therapy

  • Engwall, Erik
  • Fredriksson, Albin
  • Glimelius, Lars
Medical Physics 2018 Journal Article, cited 2 times
Website

Attention P-Net for Segmentation of Post-operative Glioblastoma in MRI

  • Enlund Åström, Isabelle
2019 Thesis, cited 0 times
Website
Segmentation of post-operative glioblastoma is important for follow-up treatment. In this thesis, Fully Convolutional Networks (FCN) are utilised together with attention modules for segmentation of post-operative glioblastoma in MR images. Attention-based modules help the FCN to focus on relevant features to improve segmentation results. Channel and spatial attention combines both the spatial context as well as the semantic information in MR images. P-Net is used as a backbone for creating an architecture with existing bottleneck attention modules and was named attention P-Net. The proposed network and competing techniques were evaluated on a Uppsala University database containing T1-weighted MR images of brain from 12 subjects. The proposed framework shows substantial improvement over the existing techniques.

Radiology and Enterprise Medical Imaging Extensions (REMIX)

  • Erdal, Barbaros S
  • Prevedello, Luciano M
  • Qian, Songyue
  • Demirer, Mutlu
  • Little, Kevin
  • Ryu, John
  • O’Donnell, Thomas
  • White, Richard D
2017 Journal Article, cited 1 times
Website

Multisite Image Data Collection and Management Using the RSNA Image Sharing Network

  • Erickson, Bradley J
  • Fajnwaks, Patricio
  • Langer, Steve G
  • Perry, John
Transl OncolTranslational oncology 2014 Journal Article, cited 3 times
Website
The execution of a multisite trial frequently includes image collection. The Clinical Trials Processor (CTP) makes removal of protected health information highly reliable. It also provides reliable transfer of images to a central review site. Trials using central review of imaging should consider using CTP for handling image data when a multisite trial is being designed.

New prognostic factor telomerase reverse transcriptase promotor mutation presents without MR imaging biomarkers in primary glioblastoma

  • Ersoy, Tunc F
  • Keil, Vera C
  • Hadizadeh, Dariusch R
  • Gielen, Gerrit H
  • Fimmers, Rolf
  • Waha, Andreas
  • Heidenreich, Barbara
  • Kumar, Rajiv
  • Schild, Hans H
  • Simon, Matthias
Neuroradiology 2017 Journal Article, cited 1 times
Website
PURPOSE: Magnetic resonance (MR) imaging biomarkers can assist in the non-invasive assessment of the genetic status in glioblastomas (GBMs). Telomerase reverse transcriptase (TERT) promoter mutations are associated with a negative prognosis. This study was performed to identify MR imaging biomarkers to forecast the TERT mutation status. METHODS: Pre-operative MRIs of 64/67 genetically confirmed primary GBM patients (51/67 TERT-mutated with rs2853669 polymorphism) were analyzed according to Visually AcceSAble Rembrandt Images (VASARI) ( https://wiki.cancerimagingarchive.net/display/Public/VASARI+Research+Project ) imaging criteria by three radiological raters. TERT mutation and O(6)-methylguanine-DNA methyltransferase (MGMT) hypermethylation data were obtained through direct and pyrosequencing as described in a previous study. Clinical data were derived from a prospectively maintained electronic database. Associations of potential imaging biomarkers and genetic status were assessed by Fisher and Mann-Whitney U tests and stepwise linear regression. RESULTS: No imaging biomarkers could be identified to predict TERT mutational status (alone or in conjunction with TERT promoter polymorphism rs2853669 AA-allele). TERT promoter mutations were more common in patients with tumor-associated seizures as first symptom (26/30 vs. 25/37, p = 0.07); these showed significantly smaller tumors [13.1 (9.0-19.0) vs. 24.0 (16.6-37.5) all cm(3); p = 0.007] and prolonged median overall survival [17.0 (11.5-28.0) vs. 9.0 (4.0-12.0) all months; p = 0.02]. TERT-mutated GBMs were underrepresented in the extended angularis region (p = 0.03), whereas MGMT-methylated GBMs were overrepresented in the corpus callosum (p = 0.03) and underrepresented temporomesially (p = 0.01). CONCLUSION: Imaging biomarkers for prediction of TERT mutation status remain weak and cannot be derived from the VASARI protocol. Tumor-associated seizures are less common in TERT mutated glioblastomas.

Computer-aided detection of Pulmonary Nodules based on SVM in thoracic CT images

  • Eskandarian, Parinaz
  • Bagherzadeh, Jamshid
2015 Conference Proceedings, cited 12 times
Website
Computer-Aided diagnosis of Solitary Pulmonary Nodules using the method of X-ray CT images is the early detection of lung cancer. In this study, a computer-aided system for detection of pulmonary nodules on CT scan based support vector machine classifier is provided for the diagnosis of solitary pulmonary nodules. So at the first step, by data mining techniques, volume of data are reduced. Then divided by the area of the chest, the suspicious nodules are identified and eventually nodules are detected. In comparison with the threshold-based methods, support vector machine classifier to classify more accurately describes areas of the lungs. In this study, the false positive rate is reduced by combination of threshold with support vector machine classifier. Experimental results based on data from 147 patients with lung LIDC image database show that the proposed system is able to obtained sensitivity of 89.9% and false positive of 3.9 per scan. In comparison to previous systems, the proposed system demonstrates good performance.

Towards Fully Automatic X-Ray to CT Registration

  • Esteban, Javier
  • Grimm, Matthias
  • Unberath, Mathias
  • Zahnd, Guillaume
  • Navab, Nassir
2019 Journal Article, cited 3 times
Website
The main challenge preventing a fully-automatic X-ray to CT registration is an initialization scheme that brings the X-ray pose within the capture range of existing intensity-based registration methods. By providing such an automatic initialization, the present study introduces the first end-to-end fully-automatic registration framework. A network is first trained once on artificial X-rays to extract 2D landmarks resulting from the projection of CT-labels. A patient-specific refinement scheme is then carried out: candidate points detected from a new set of artificial X-rays are back-projected onto the patient CT and merged into a refined meaningful set of landmarks used for network re-training. This network-landmarks combination is finally exploited for intraoperative pose-initialization with a runtime of 102 ms. Evaluated on 6 pelvis anatomies (486 images in total), the mean Target Registration Error was 15.0±7.3 mm. When used to initialize the BOBYQA optimizer with normalized cross-correlation, the average (± STD) projection distance was 3.4±2.3 mm, and the registration success rate (projection distance <2.5% of the detector width) greater than 97%.

Deep Learning-Based Concurrent Brain Registration and Tumor Segmentation

  • Estienne, T.
  • Lerousseau, M.
  • Vakalopoulou, M.
  • Alvarez Andres, E.
  • Battistella, E.
  • Carre, A.
  • Chandra, S.
  • Christodoulidis, S.
  • Sahasrabudhe, M.
  • Sun, R.
  • Robert, C.
  • Talbot, H.
  • Paragios, N.
  • Deutsch, E.
Front Comput Neurosci 2020 Journal Article, cited 15 times
Website
Image registration and segmentation are the two most studied problems in medical image analysis. Deep learning algorithms have recently gained a lot of attention due to their success and state-of-the-art results in variety of problems and communities. In this paper, we propose a novel, efficient, and multi-task algorithm that addresses the problems of image registration and brain tumor segmentation jointly. Our method exploits the dependencies between these tasks through a natural coupling of their interdependencies during inference. In particular, the similarity constraints are relaxed within the tumor regions using an efficient and relatively simple formulation. We evaluated the performance of our formulation both quantitatively and qualitatively for registration and segmentation problems on two publicly available datasets (BraTS 2018 and OASIS 3), reporting competitive results with other recent state-of-the-art methods. Moreover, our proposed framework reports significant amelioration (p < 0.005) for the registration performance inside the tumor locations, providing a generic method that does not need any predefined conditions (e.g., absence of abnormalities) about the volumes to be registered. Our implementation is publicly available online at https://github.com/TheoEst/joint_registration_tumor_segmentation.

Detection of effective genes in colon cancer: A machine learning approach

  • Fahami, Mohammad Amin
  • Roshanzamir, Mohamad
  • Izadi, Navid Hoseini
  • Keyvani, Vahideh
  • Alizadehsani, Roohallah
Informatics in Medicine Unlocked 2021 Journal Article, cited 0 times
Website
Nowadays, a variety of cancers have become common among humans which unfortunately are the cause of death for many of these people. Early detection and diagnosis of cancers can have a significant impact on the survival of patients and treatment cost reduction. Colon cancer is the third and the second main cause of women's and men's death worldwide among cancers. Hence, many researchers have been trying to provide new methods for early diagnosis of colon cancer. In this study, we apply statistical hypothesis tests such as t-test and Mann–Whitney–Wilcoxon and machine learning methods such as Neural Network, KNN and Decision Tree to detect the most effective genes in the vital status of colon cancer patients. We normalize the dataset using a new two-step method. In the first step, the genes within each sample (patient) are normalized to have zero mean and unit variance. In the second step, normalization is done for each gene across the whole dataset. Analyzing the results shows that this normalization method is more efficient than the others and improves the overall performance of the research. Afterwards, we apply unsupervised learning methods to find the meaningful structures in colon cancer gene expressions. In this regard, the dimensionality of the dataset is reduced by employing Principle Component Analysis (PCA). Next, we cluster the patients according to the PCA extracted features. We then check the labeling results of unsupervised learning methods using different supervised learning algorithms. Finally, we determine genes which have major impact on colon cancer mortality rate in each cluster. Our conducted study is the first which suggests that the colon cancer patients can be categorized into two clusters. In each cluster, 20 effective genes were extracted which can be important for early diagnosis of colon cancer. Many of these genes have been identified for the first time.

Tumour heterogeneity revealed by unsupervised decomposition of dynamic contrast-enhanced magnetic resonance imaging is associated with underlying gene expression patterns and poor survival in breast cancer patients

  • Fan, M.
  • Xia, P.
  • Liu, B.
  • Zhang, L.
  • Wang, Y.
  • Gao, X.
  • Li, L.
Breast Cancer Res 2019 Journal Article, cited 3 times
Website
BACKGROUND: Heterogeneity is a common finding within tumours. We evaluated the imaging features of tumours based on the decomposition of tumoural dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data to identify their prognostic value for breast cancer survival and to explore their biological importance. METHODS: Imaging features (n = 14), such as texture, histogram distribution and morphological features, were extracted to determine their associations with recurrence-free survival (RFS) in patients in the training cohort (n = 61) from The Cancer Imaging Archive (TCIA). The prognostic value of the features was evaluated in an independent dataset of 173 patients (i.e. the reproducibility cohort) from the TCIA I-SPY 1 TRIAL dataset. Radiogenomic analysis was performed in an additional cohort, the radiogenomic cohort (n = 87), using DCE-MRI from TCGA-BRCA and corresponding gene expression data from The Cancer Genome Atlas (TCGA). The MRI tumour area was decomposed by convex analysis of mixtures (CAM), resulting in 3 components that represent plasma input, fast-flow kinetics and slow-flow kinetics. The prognostic MRI features were associated with the gene expression module in which the pathway was analysed. Furthermore, a multigene signature for each prognostic imaging feature was built, and the prognostic value for RFS and overall survival (OS) was confirmed in an additional cohort from TCGA. RESULTS: Three image features (i.e. the maximum probability from the precontrast MR series, the median value from the second postcontrast series and the overall tumour volume) were independently correlated with RFS (p values of 0.0018, 0.0036 and 0.0032, respectively). The maximum probability feature from the fast-flow kinetics subregion was also significantly associated with RFS and OS in the reproducibility cohort. Additionally, this feature had a high correlation with the gene expression module (r = 0.59), and the pathway analysis showed that Ras signalling, a breast cancer-related pathway, was significantly enriched (corrected p value = 0.0044). Gene signatures (n = 43) associated with the maximum probability feature were assessed for associations with RFS (p = 0.035) and OS (p = 0.027) in an independent dataset containing 1010 gene expression samples. Among the 43 gene signatures, Ras signalling was also significantly enriched. CONCLUSIONS: Dynamic pattern deconvolution revealed that tumour heterogeneity was associated with poor survival and cancer-related pathways in breast cancer.

EGFR/SRC/ERK-stabilized YTHDF2 promotes cholesterol dysregulation and invasive growth of glioblastoma

  • Fang, Runping
  • Chen, Xin
  • Zhang, Sicong
  • Shi, Hui
  • Ye, Youqiong
  • Shi, Hailing
  • Zou, Zhongyu
  • Li, Peng
  • Guo, Qing
  • Ma, Li
Nature Communications 2021 Journal Article, cited 14 times
Website

Resolution enhancement for lung 4D-CT based on transversal structures by using multiple Gaussian process regression learning

  • Fang, Shiting
  • Hu, Runyue
  • Yuan, Xinrui
  • Liu, Shangqing
  • Zhang, Yuan
Phys Med 2020 Journal Article, cited 0 times
Website
PURPOSE: Four-dimensional computed tomography (4D-CT) plays a useful role in many clinical situations. However, due to the hardware limitation of system, dense sampling along superior-inferior direction is often not practical. In this paper, we develop a novel multiple Gaussian process regression model to enhance the superior-inferior resolution for lung 4D-CT based on transversal structures. METHODS: The proposed strategy is based on the observation that high resolution transversal images can recover missing pixels in the superior-inferior direction. Based on this observation and motived by random forest algorithm, we employ multiple Gaussian process regression model learned from transversal images to improve superior-inferior resolution. Specifically, we first randomly sample 3 x 3 patches from original transversal images. The central pixel of these patches and the eight-neighbour pixels of their corresponding degraded versions form the label and input of training data, respectively. Multiple Gaussian process regression model is then built on the basis of multiple training subsets obtained by random sampling. Finally, the central pixel of the patch is estimated based on the proposed model, with the eight-neighbour pixels of each 3 x 3 patch from interpolated superior-inferior direction images as inputs. RESULTS: The performance of our method is extensively evaluated using simulated and publicly available datasets. Our experiments show the remarkable performance of the proposed method. CONCLUSIONS: In this paper, we propose a new approach to improve the 4D-CT resolution, which does not require any external data and hardware support, and can produce clear coronal/sagittal images for easy viewing.

Feature fusion for lung nodule classification

  • Farag, Amal A
  • Ali, Asem
  • Elshazly, Salwa
  • Farag, Aly A
International Journal of Computer Assisted Radiology and Surgery 2017 Journal Article, cited 3 times
Website

Hybrid intelligent approach for diagnosis of the lung nodule from CT images using spatial kernelized fuzzy c-means and ensemble learning

  • Farahani, Farzad Vasheghani
  • Ahmadi, Abbas
  • Zarandi, Mohammad Hossein Fazel
Mathematics and Computers in Simulation 2018 Journal Article, cited 1 times
Website

Computational Challenges and Collaborative Projects in the NCI Quantitative Imaging Network

  • Farahani, Keyvan
  • Kalpathy-Cramer, Jayashree
  • Chenevert, Thomas L
  • Rubin, Daniel L
  • Sunderland, John J
  • Nordstrom, Robert J
  • Buatti, John
  • Hylton, Nola
Tomography 2016 Journal Article, cited 2 times
Website
The Quantitative Imaging Network (QIN) of the National Cancer Institute (NCI) conducts research in development and validation of imaging tools and methods for predicting and evaluating clinical response to cancer therapy. Members of the network are involved in examining various imaging and image assessment parameters through network-wide cooperative projects. To more effectively use the cooperative power of the network in conducting computational challenges in benchmarking of tools and methods and collaborative projects in analytical assessment of imaging technologies, the QIN Challenge Task Force has developed policies and procedures to enhance the value of these activities by developing guidelines and leveraging NCI resources to help their administration and manage dissemination of results. Challenges and Collaborative Projects (CCPs) are further divided into technical and clinical CCPs. As the first NCI network to engage in CCPs, we anticipate a variety of CCPs to be conducted by QIN teams in the coming years. These will be aimed to benchmark advanced software tools for clinical decision support, explore new imaging biomarkers for therapeutic assessment, and establish consensus on a range of methods and protocols in support of the use of quantitative imaging to predict and assess response to cancer therapy.

Recurrent Attention Network for False Positive Reduction in the Detection of Pulmonary Nodules in Thoracic CT Scans

  • M. Mehdi Farhangi
  • Nicholas Petrick
  • Berkman Sahiner
  • Hichem Frigui
  • Amir A. Amini
  • Aria Pezeshk
Med Phys 2020 Journal Article, cited 0 times
Website
PURPOSE: Multi-view 2-D Convolutional Neural Networks (CNNs) and 3-D CNNs have been successfully used for analyzing volumetric data in many state-of-the-art medical imaging applications. We propose an alternative modular framework that analyzes volumetric data with an approach that is analogous to radiologists' interpretation, and apply the framework to reduce false positives that are generated in Computer-Aided Detection (CADe) systems for pulmonary nodules in thoracic CT scans. METHODS: In our approach, a deep network consisting of 2-D CNNs first processes slices individually. The features extracted in this stage are then passed to a Recurrent Neural Network (RNN), thereby modeling consecutive slices as a sequence of temporal data and capturing the contextual information across all three dimensions in the volume of interest. Outputs of the RNN layer are weighed before the final fully connected layer, enabling the network to scale the importance of different slices within a volume of interest in an end-to-end training framework. RESULTS: We validated the proposed architecture on the false positive reduction track of the Lung Nodule Analysis (LUNA) challenge for pulmonary nodule detection in chest CT scans, and obtained competitive results compared to 3-D CNNs. Our results show that the proposed approach can encode the 3-D information in volumetric data effectively by achieving a sensitivity > 0.8 with just 1/8 false positives per scan. CONCLUSIONS: Our experimental results demonstrate the effectiveness of temporal analysis of volumetric images for the application of false positive reduction in chest CT scans and show that state-of-the-art 2-D architectures from the literature can be directly applied to analyzing volumetric medical data. As newer and better 2-D architectures are being developed at a much faster rate compared to 3-D architectures, our approach makes it easy to obtain state-of-the-art performance on volumetric data using new 2-D architectures.

A study of machine learning and deep learning models for solving medical imaging problems

  • Farhat, Fadi G.
2019 Thesis, cited 0 times
Website
Application of machine learning and deep learning methods on medical imaging aims to create systems that can help in the diagnosis of disease and the automation of analyzing medical images in order to facilitate treatment planning. Deep learning methods do well in image recognition, but medical images present unique challenges. The lack of large amounts of data, the image size, and the high class-imbalance in most datasets, makes training a machine learning model to recognize a particular pattern that is typically present only in case images a formidable task. Experiments are conducted to classify breast cancer images as healthy or nonhealthy, and to detect lesions in damaged brain MRI (Magnetic Resonance Imaging) scans. Random Forest, Logistic Regression and Support Vector Machine perform competitively in the classification experiments, but in general, deep neural networks beat all conventional methods. Gaussian Naïve Bayes (GNB) and the Lesion Identification with Neighborhood Data Analysis (LINDA) methods produce better lesion detection results than single path neural networks, but a multi-modal, multi-path deep neural network beats all other methods. The importance of pre-processing training data is also highlighted and demonstrated, especially for medical images, which require extensive preparation to improve classifier and detector performance. Only a more complex and deeper neural network combined with properly pre-processed data can produce the desired accuracy levels that can rival and maybe exceed those of human experts.

Signal intensity analysis of ecological defined habitat in soft tissue sarcomas to predict metastasis development

  • Farhidzadeh, Hamidreza
  • Chaudhury, Baishali
  • Scott, Jacob G
  • Goldgof, Dmitry B
  • Hall, Lawrence O
  • Gatenby, Robert A
  • Gillies, Robert J
  • Raghavan, Meera
2016 Conference Proceedings, cited 6 times
Website

Quantitative Imaging Informatics for Cancer Research

  • Fedorov, Andrey
  • Beichel, Reinhard
  • Kalpathy-Cramer, Jayashree
  • Clunie, David
  • Onken, Michael
  • Riesmeier, Jorg
  • Herz, Christian
  • Bauer, Christian
  • Beers, Andrew
  • Fillion-Robin, Jean-Christophe
  • Lasso, Andras
  • Pinter, Csaba
  • Pieper, Steve
  • Nolden, Marco
  • Maier-Hein, Klaus
  • Herrmann, Markus D
  • Saltz, Joel
  • Prior, Fred
  • Fennessy, Fiona
  • Buatti, John
  • Kikinis, Ron
JCO Clin Cancer Inform 2020 Journal Article, cited 0 times
Website
PURPOSE: We summarize Quantitative Imaging Informatics for Cancer Research (QIICR; U24 CA180918), one of the first projects funded by the National Cancer Institute (NCI) Informatics Technology for Cancer Research program. METHODS: QIICR was motivated by the 3 use cases from the NCI Quantitative Imaging Network. 3D Slicer was selected as the platform for implementation of open-source quantitative imaging (QI) tools. Digital Imaging and Communications in Medicine (DICOM) was chosen for standardization of QI analysis outputs. Support of improved integration with community repositories focused on The Cancer Imaging Archive (TCIA). Priorities included improved capabilities of the standard, toolkits and tools, reference datasets, collaborations, and training and outreach. RESULTS: Fourteen new tools to support head and neck cancer, glioblastoma, and prostate cancer QI research were introduced and downloaded over 100,000 times. DICOM was amended, with over 40 correction proposals addressing QI needs. Reference implementations of the standard in a popular toolkit and standalone tools were introduced. Eight datasets exemplifying the application of the standard and tools were contributed. An open demonstration/connectathon was organized, attracting the participation of academic groups and commercial vendors. Integration of tools with TCIA was improved by implementing programmatic communication interface and by refining best practices for QI analysis results curation. CONCLUSION: Tools, capabilities of the DICOM standard, and datasets we introduced found adoption and utility within the cancer imaging community. A collaborative approach is critical to addressing challenges in imaging informatics at the national and international levels. Numerous challenges remain in establishing and maintaining the infrastructure of analysis tools and standardized datasets for the imaging community. Ideas and technology developed by the QIICR project are contributing to the NCI Imaging Data Commons currently being developed.

DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research

  • Fedorov, Andriy
  • Clunie, David
  • Ulrich, Ethan
  • Bauer, Christian
  • Wahle, Andreas
  • Brown, Bartley
  • Onken, Michael
  • Riesmeier, Jörg
  • Pieper, Steve
  • Kikinis, Ron
  • Buatti, John
  • Beichel, Reinhard R
PeerJ 2016 Journal Article, cited 20 times
Website
Background. Imaging biomarkers hold tremendous promise for precision medicine clinical applications. Development of such biomarkers relies heavily on image post-processing tools for automated image quantitation. Their deployment in the context of clinical research necessitates interoperability with the clinical systems. Comparison with the established outcomes and evaluation tasks motivate integration of the clinical and imaging data, and the use of standardized approaches to support annotation and sharing of the analysis results and semantics. We developed the methodology and tools to support these tasks in Positron Emission Tomography and Computed Tomography (PET/CT) quantitative imaging (QI) biomarker development applied to head and neck cancer (HNC) treatment response assessment, using the Digital Imaging and Communications in Medicine (DICOM((R))) international standard and free open-source software. Methods. Quantitative analysis of PET/CT imaging data collected on patients undergoing treatment for HNC was conducted. Processing steps included Standardized Uptake Value (SUV) normalization of the images, segmentation of the tumor using manual and semi-automatic approaches, automatic segmentation of the reference regions, and extraction of the volumetric segmentation-based measurements. Suitable components of the DICOM standard were identified to model the various types of data produced by the analysis. A developer toolkit of conversion routines and an Application Programming Interface (API) were contributed and applied to create a standards-based representation of the data. Results. DICOM Real World Value Mapping, Segmentation and Structured Reporting objects were utilized for standards-compliant representation of the PET/CT QI analysis results and relevant clinical data. A number of correction proposals to the standard were developed. The open-source DICOM toolkit (DCMTK) was improved to simplify the task of DICOM encoding by introducing new API abstractions. Conversion and visualization tools utilizing this toolkit were developed. The encoded objects were validated for consistency and interoperability. The resulting dataset was deposited in the QIN-HEADNECK collection of The Cancer Imaging Archive (TCIA). Supporting tools for data analysis and DICOM conversion were made available as free open-source software. Discussion. We presented a detailed investigation of the development and application of the DICOM model, as well as the supporting open-source tools and toolkits, to accommodate representation of the research data in QI biomarker development. We demonstrated that the DICOM standard can be used to represent the types of data relevant in HNC QI biomarker development, and encode their complex relationships. The resulting annotated objects are amenable to data mining applications, and are interoperable with a variety of systems that support the DICOM standard.

A comparison of two methods for estimating DCE-MRI parameters via individual and cohort based AIFs in prostate cancer: A step towards practical implementation

  • Fedorov, Andriy
  • Fluckiger, Jacob
  • Ayers, Gregory D
  • Li, Xia
  • Gupta, Sandeep N
  • Tempany, Clare
  • Mulkern, Robert
  • Yankeelov, Thomas E
  • Fennessy, Fiona M
Magnetic resonance imaging 2014 Journal Article, cited 30 times
Website
Multi-parametric Magnetic Resonance Imaging, and specifically Dynamic Contrast Enhanced (DCE) MRI, play increasingly important roles in detection and staging of prostate cancer (PCa). One of the actively investigated approaches to DCE MRI analysis involves pharmacokinetic (PK) modeling to extract quantitative parameters that may be related to microvascular properties of the tissue. It is well-known that the prescribed arterial blood plasma concentration (or Arterial Input Function, AIF) input can have significant effects on the parameters estimated by PK modeling. The purpose of our study was to investigate such effects in DCE MRI data acquired in a typical clinical PCa setting. First, we investigated how the choice of a semi-automated or fully automated image-based individualized AIF (iAIF) estimation method affects the PK parameter values; and second, we examined the use of method-specific averaged AIF (cohort-based, or cAIF) as a means to attenuate the differences between the two AIF estimation methods. Two methods for automated image-based estimation of individualized (patient-specific) AIFs, one of which was previously validated for brain and the other for breast MRI, were compared. cAIFs were constructed by averaging the iAIF curves over the individual patients for each of the two methods. Pharmacokinetic analysis using the Generalized kinetic model and each of the four AIF choices (iAIF and cAIF for each of the two image-based AIF estimation approaches) was applied to derive the volume transfer rate (K(trans)) and extravascular extracellular volume fraction (ve) in the areas of prostate tumor. Differences between the parameters obtained using iAIF and cAIF for a given method (intra-method comparison) as well as inter-method differences were quantified. The study utilized DCE MRI data collected in 17 patients with histologically confirmed PCa. Comparison at the level of the tumor region of interest (ROI) showed that the two automated methods resulted in significantly different (p<0.05) mean estimates of ve, but not of K(trans). Comparing cAIF, different estimates for both ve, and K(trans) were obtained. Intra-method comparison between the iAIF- and cAIF-driven analyses showed the lack of effect on ve, while K(trans) values were significantly different for one of the methods. Our results indicate that the choice of the algorithm used for automated image-based AIF determination can lead to significant differences in the values of the estimated PK parameters. K(trans) estimates are more sensitive to the choice between cAIF/iAIF as compared to ve, leading to potentially significant differences depending on the AIF method. These observations may have practical consequences in evaluating the PK analysis results obtained in a multi-site setting.

An annotated test-retest collection of prostate multiparametric MRI

  • Fedorov, Andriy
  • Schwier, Michael
  • Clunie, David
  • Herz, Christian
  • Pieper, Steve
  • Kikinis, Ron
  • Tempany, Clare
  • Fennessy, Fiona
Scientific data 2018 Journal Article, cited 0 times
Website

Comparison of methods for sensitivity correction in Talbot–Lau computed tomography

  • Felsner, Lina
  • Roser, Philipp
  • Maier, Andreas
  • Riess, Christian
International Journal of Computer Assisted Radiology and Surgery 2021 Journal Article, cited 0 times
Website

Identifying BAP1 Mutations in Clear-Cell Renal Cell Carcinoma by CT Radiomics: Preliminary Findings

  • Feng, Zhan
  • Zhang, Lixia
  • Qi, Zhong
  • Shen, Qijun
  • Hu, Zhengyu
  • Chen, Feng
Frontiers in Oncology 2020 Journal Article, cited 0 times
Website
To evaluate the potential application of computed tomography (CT) radiomics in the prediction of BRCA1-associated protein 1 (BAP1) mutation status in patients with clear-cell renal cell carcinoma (ccRCC). In this retrospective study, clinical and CT imaging data of 54 patients were retrieved from The Cancer Genome Atlas–Kidney Renal Clear Cell Carcinoma database. Among these, 45 patients had wild-type BAP1 and nine patients had BAP1 mutation. The texture features of tumor images were extracted using the Matlab-based IBEX package. To produce class-balanced data and improve the stability of prediction, we performed data augmentation for the BAP1 mutation group during cross validation. A model to predict BAP1 mutation status was constructed using Random Forest Classification algorithms, and was evaluated using leave-one-out-cross-validation. Random Forest model of predict BAP1 mutation status had an accuracy of 0.83, sensitivity of 0.72, specificity of 0.87, precision of 0.65, AUC of 0.77, F-score of 0.68. CT radiomics is a potential and feasible method for predicting BAP1 mutation status in patients with ccRCC.

Deep Learning Model for Automatic Contouring of Cardiovascular Substructures on Radiotherapy Planning CT Images: Dosimetric Validation and Reader Study based Clinical Acceptability Testing

  • Fernandes, Miguel Garrett
  • Bussink, Johan
  • Stam, Barbara
  • Wijsman, Robin
  • Schinagl, Dominic AX
  • Teuwen, Jonas
  • Monshouwer, René
Radiotherapy and Oncology 2021 Journal Article, cited 0 times
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HEVC optimizations for medical environments

  • Fernández, DG
  • Del Barrio, AA
  • Botella, Guillermo
  • García, Carlos
  • Meyer-Baese, Uwe
  • Meyer-Baese, Anke
2016 Conference Proceedings, cited 5 times
Website

Characterization of Pulmonary Nodules Based on Features of Margin Sharpness and Texture

  • Ferreira, José Raniery
  • Oliveira, Marcelo Costa
  • de Azevedo-Marques, Paulo Mazzoncini
2017 Journal Article, cited 1 times
Website

On the Evaluation of the Suitability of the Materials Used to 3D Print Holographic Acoustic Lenses to Correct Transcranial Focused Ultrasound Aberrations

  • Ferri, Marcelino
  • Bravo, Jose Maria
  • Redondo, Javier
  • Jimenez-Gambin, Sergio
  • Jimenez, Noe
  • Camarena, Francisco
  • Sanchez-Perez, Juan Vicente
Polymers (Basel) 2019 Journal Article, cited 2 times
Website
The correction of transcranial focused ultrasound aberrations is a relevant topic for enhancing various non-invasive medical treatments. Presently, the most widely accepted method to improve focusing is the emission through multi-element phased arrays; however, a new disruptive technology, based on 3D printed holographic acoustic lenses, has recently been proposed, overcoming the spatial limitations of phased arrays due to the submillimetric precision of the latest generation of 3D printers. This work aims to optimize this recent solution. Particularly, the preferred acoustic properties of the polymers used for printing the lenses are systematically analyzed, paying special attention to the effect of p-wave speed and its relationship to the achievable voxel size of 3D printers. Results from simulations and experiments clearly show that, given a particular voxel size, there are optimal ranges for lens thickness and p-wave speed, fairly independent of the emitted frequency, the transducer aperture, or the transducer-target distance.

Enhanced Numerical Method for the Design of 3-D-Printed Holographic Acoustic Lenses for Aberration Correction of Single-Element Transcranial Focused Ultrasound

  • Marcelino Ferri
  • José M. Bravo
  • Javier Redondo
  • Juan V. Sánchez-Pérez
Ultrasound in Medicine & Biology 2018 Journal Article, cited 0 times
Website
The correction of transcranial focused ultrasound aberrations is a relevant issue for enhancing various non-invasive medical treatments. The emission through multi-element phased arrays has been the most widely accepted method to improve focusing in recent years; however, the number and size of transducers represent a bottleneck that limits the focusing accuracy of the technique. To overcome this limitation, a new disruptive technology, based on 3-D-printed acoustic lenses, has recently been proposed. As the submillimeter precision of the latest generation of 3-D printers has been proven to overcome the spatial limitations of phased arrays, a new challenge is to improve the accuracy of the numerical simulations required to design this type of ultrasound lens. In the study described here, we evaluated two improvements in the numerical model applied in previous works for the design of 3-D-printed lenses: (i) allowing the propagation of shear waves in the skull by means of its simulation as an isotropic solid and (ii) introduction of absorption into the set of equations that describes the dynamics of the wave in both fluid and solid media. The results obtained in the numerical simulations are evidence that the inclusion of both s-waves and absorption significantly improves focusing.

LCD-OpenPACS: sistema integrado de telerradiologia com auxílio ao diagnóstico de nódulos pulmonares em exames de tomografia computadorizada

  • Firmino Filho, José Macêdo
2015 Thesis, cited 1 times
Website

Computer-aided detection (CADe) and diagnosis (CADx) system for lung cancer with likelihood of malignancy

  • Firmino, Macedo
  • Angelo, Giovani
  • Morais, Higor
  • Dantas, Marcel R
  • Valentim, Ricardo
BioMedical Engineering OnLine 2016 Journal Article, cited 63 times
Website
BACKGROUND: CADe and CADx systems for the detection and diagnosis of lung cancer have been important areas of research in recent decades. However, these areas are being worked on separately. CADe systems do not present the radiological characteristics of tumors, and CADx systems do not detect nodules and do not have good levels of automation. As a result, these systems are not yet widely used in clinical settings. METHODS: The purpose of this article is to develop a new system for detection and diagnosis of pulmonary nodules on CT images, grouping them into a single system for the identification and characterization of the nodules to improve the level of automation. The article also presents as contributions: the use of Watershed and Histogram of oriented Gradients (HOG) techniques for distinguishing the possible nodules from other structures and feature extraction for pulmonary nodules, respectively. For the diagnosis, it is based on the likelihood of malignancy allowing more aid in the decision making by the radiologists. A rule-based classifier and Support Vector Machine (SVM) have been used to eliminate false positives. RESULTS: The database used in this research consisted of 420 cases obtained randomly from LIDC-IDRI. The segmentation method achieved an accuracy of 97 % and the detection system showed a sensitivity of 94.4 % with 7.04 false positives per case. Different types of nodules (isolated, juxtapleural, juxtavascular and ground-glass) with diameters between 3 mm and 30 mm have been detected. For the diagnosis of malignancy our system presented ROC curves with areas of: 0.91 for nodules highly unlikely of being malignant, 0.80 for nodules moderately unlikely of being malignant, 0.72 for nodules with indeterminate malignancy, 0.67 for nodules moderately suspicious of being malignant and 0.83 for nodules highly suspicious of being malignant. CONCLUSIONS: From our preliminary results, we believe that our system is promising for clinical applications assisting radiologists in the detection and diagnosis of lung cancer.

A Radiogenomic Approach for Decoding Molecular Mechanisms Underlying Tumor Progression in Prostate Cancer

  • Fischer, Sarah
  • Tahoun, Mohamed
  • Klaan, Bastian
  • Thierfelder, Kolja M
  • Weber, Marc-Andre
  • Krause, Bernd J
  • Hakenberg, Oliver
  • Fuellen, Georg
  • Hamed, Mohamed
Cancers (Basel) 2019 Journal Article, cited 0 times
Website
Prostate cancer (PCa) is a genetically heterogeneous cancer entity that causes challenges in pre-treatment clinical evaluation, such as the correct identification of the tumor stage. Conventional clinical tests based on digital rectal examination, Prostate-Specific Antigen (PSA) levels, and Gleason score still lack accuracy for stage prediction. We hypothesize that unraveling the molecular mechanisms underlying PCa staging via integrative analysis of multi-OMICs data could significantly improve the prediction accuracy for PCa pathological stages. We present a radiogenomic approach comprising clinical, imaging, and two genomic (gene and miRNA expression) datasets for 298 PCa patients. Comprehensive analysis of gene and miRNA expression profiles for two frequent PCa stages (T2c and T3b) unraveled the molecular characteristics for each stage and the corresponding gene regulatory interaction network that may drive tumor upstaging from T2c to T3b. Furthermore, four biomarkers (ANPEP, mir-217, mir-592, mir-6715b) were found to distinguish between the two PCa stages and were highly correlated (average r = +/- 0.75) with corresponding aggressiveness-related imaging features in both tumor stages. When combined with related clinical features, these biomarkers markedly improved the prediction accuracy for the pathological stage. Our prediction model exhibits high potential to yield clinically relevant results for characterizing PCa aggressiveness.

The ASNR-ACR-RSNA Common Data Elements Project: What Will It Do for the House of Neuroradiology?

  • Flanders, AE
  • Jordan, JE
American Journal of Neuroradiology 2018 Journal Article, cited 0 times
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Computer-aided nodule assessment and risk yield risk management of adenocarcinoma: the future of imaging?

  • Foley, Finbar
  • Rajagopalan, Srinivasan
  • Raghunath, Sushravya M
  • Boland, Jennifer M
  • Karwoski, Ronald A
  • Maldonado, Fabien
  • Bartholmai, Brian J
  • Peikert, Tobias
2016 Conference Proceedings, cited 7 times
Website

Breast Lesion Segmentation in DCE- MRI Imaging

  • Frackiewicz, Mariusz
  • Koper, Zuzanna
  • Palus, Henryk
  • Borys, Damian
  • Psiuk-Maksymowicz, Krzysztof
2018 Conference Proceedings, cited 0 times
Website
Breast cancer is one of the most common cancers in women. Typically, the course of the disease is asymptomatic in the early stages of breast cancer. Imaging breast examinations allow early detection of the cancer, which is associated with increased chances of a complete cure. There are many breast imaging techniques such as: mammography (MM), ultrasound imaging (US), positron-emission tomography (PET), computed tomography (CT), and magnetic resonance imaging (MRI). These imaging techniques differ in terms of effectiveness, price, type of physical phenomenon, the impact on the patient and its availability. In this paper, we focus on MRI imaging and we compare three breast lesion segmentation algorithms that have been tested on QIN Breast DCE-MRI database, which is publicly available. The obtained values of Dice and Jaccard indices indicate the segmentation using k-means algorithm.

Classification of COVID-19 in chest radiographs: assessing the impact of imaging parameters using clinical and simulated images

  • Fricks, Rafael
  • Abadi, Ehsan
  • Ria, Francesco
  • Samei, Ehsan
  • Drukker, Karen
  • Mazurowski, Maciej A.
2021 Conference Paper, cited 1 times
Website
As computer-aided diagnostics develop to address new challenges in medical imaging, including emerging diseases such as COVID-19, the initial development is hampered by availability of imaging data. Deep learning algorithms are particularly notorious for performance that tends to improve proportionally to the amount of available data. Simulated images, as available through advanced virtual trials, may present an alternative in data-constrained applications. We begin with our previously trained COVID-19 x-ray classification model (denoted as CVX) that leveraged additional training with existing pre-pandemic chest radiographs to improve classification performance in a set of COVID-19 chest radiographs. The CVX model achieves demonstrably better performance on clinical images compared to an equivalent model that applies standard transfer learning from ImageNet weights. The higher performing CVX model is then shown to generalize effectively to a set of simulated COVID-19 images, both quantitative comparisons of AUCs from clinical to simulated image sets, but also in a qualitative sense where saliency map patterns are consistent when compared between sets. We then stratify the classification results in simulated images to examine dependencies in imaging parameters when patient features are constant. Simulated images show promise in optimizing imaging parameters for accurate classification in data-constrained applications.

Supervised Machine-Learning Framework and Classifier Evaluation for Automated Three-dimensional Medical Image Segmentation based on Body MRI

  • Frischmann, Patrick
2013 Thesis, cited 0 times
Website

A novel approach to 2D/3D registration of X-ray images using Grangeat's relation

  • Frysch, R.
  • Pfeiffer, T.
  • Rose, G.
Med Image Anal 2020 Journal Article, cited 0 times
Website
Fast and accurate 2D/3D registration plays an important role in many applications, ranging from scientific and engineering domains all the way to medical care. Today's predominant methods are based on computationally expensive approaches, such as virtual forward or back projections, that limit the real-time applicability of the routines. Here, we present a novel concept that makes use of Grangeat's relation to intertwine information from the 3D volume and the 2D projection space in a way that allows pre-computation of all time-intensive steps. The main effort within actual registration tasks is reduced to simple resampling of the pre-calculated values, which can be executed rapidly on modern GPU hardware. We analyze the applicability of the proposed method on simulated data under various conditions and evaluate the findings on real data from a C-arm CT scanner. Our results show high registration quality in both simulated as well as real data scenarios and demonstrate a reduction in computation time for the crucial computation step by a factor of six to eight when compared to state-of-the-art routines. With minor trade-offs in accuracy, this speed-up can even be increased up to a factor of 100 in particular settings. To our knowledge, this is the first application of Grangeat's relation to the topic of 2D/3D registration. Due to its high computational efficiency and broad range of potential applications, we believe it constitutes a highly relevant approach for various problems dealing with cone beam transmission images.

Automatic Detection of Lung Nodules Using 3D Deep Convolutional Neural Networks

  • Fu, Ling
  • Ma, Jingchen
  • Chen, Yizhi
  • Larsson, Rasmus
  • Zhao, Jun
Journal of Shanghai Jiaotong University (Science) 2019 Journal Article, cited 0 times
Website
Lung cancer is the leading cause of cancer deaths worldwide. Accurate early diagnosis is critical in increasing the 5-year survival rate of lung cancer, so the efficient and accurate detection of lung nodules, the potential precursors to lung cancer, is paramount. In this paper, a computer-aided lung nodule detection system using 3D deep convolutional neural networks (CNNs) is developed. The first multi-scale 11-layer 3D fully convolutional neural network (FCN) is used for screening all lung nodule candidates. Considering relative small sizes of lung nodules and limited memory, the input of the FCN consists of 3D image patches rather than of whole images. The candidates are further classified in the second CNN to get the final result. The proposed method achieves high performance in the LUNA16 challenge and demonstrates the effectiveness of using 3D deep CNNs for lung nodule detection.

Textural radiomic features and time-intensity curve data analysis by dynamic contrast-enhanced MRI for early prediction of breast cancer therapy response: preliminary data

  • Fusco, Roberta
  • Granata, Vincenza
  • Maio, Francesca
  • Sansone, Mario
  • Petrillo, Antonella
Eur Radiol Exp 2020 Journal Article, cited 1 times
Website
BACKGROUND: To investigate the potential of semiquantitative time-intensity curve parameters compared to textural radiomic features on arterial phase images by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) for early prediction of breast cancer neoadjuvant therapy response. METHODS: A retrospective study of 45 patients subjected to DCE-MRI by public datasets containing examination performed prior to the start of treatment and after the treatment first cycle ('QIN Breast DCE-MRI' and 'QIN-Breast') was performed. In total, 11 semiquantitative parameters and 50 texture features were extracted. Non-parametric test, receiver operating characteristic analysis with area under the curve (ROC-AUC), Spearman correlation coefficient, and Kruskal-Wallis test with Bonferroni correction were applied. RESULTS: Fifteen patients with pathological complete response (pCR) and 30 patients with non-pCR were analysed. Significant differences in median values between pCR patients and non-pCR patients were found for entropy, long-run emphasis, and busyness among the textural features, for maximum signal difference, washout slope, washin slope, and standardised index of shape among the dynamic semiquantitative parameters. The standardised index of shape had the best results with a ROC-AUC of 0.93 to differentiate pCR versus non-pCR patients. CONCLUSIONS: The standardised index of shape could become a clinical tool to differentiate, in the early stages of treatment, responding to non-responding patients.

A fast and scalable method for quality assurance of deformable image registration on lung CT scans using convolutional neural networks

  • Galib, Shaikat M
  • Lee, Hyoung K
  • Guy, Christopher L
  • Riblett, Matthew J
  • Hugo, Geoffrey D
Med Phys 2020 Journal Article, cited 1 times
Website
PURPOSE: To develop and evaluate a method to automatically identify and quantify deformable image registration (DIR) errors between lung computed tomography (CT) scans for quality assurance (QA) purposes. METHODS: We propose a deep learning method to flag registration errors. The method involves preparation of a dataset for machine learning model training and testing, design of a three-dimensional (3D) convolutional neural network architecture that classifies registrations into good or poor classes, and evaluation of a metric called registration error index (REI) which provides a quantitative measure of registration error. RESULTS: Our study shows that, despite having limited number of training images available (10 CT scan pairs for training and 17 CT scan pairs for testing), the method achieves 0.882 AUC-ROC on the test dataset. Furthermore, the combined standard uncertainty of the estimated REI by our model lies within +/- 0.11 (+/- 11% of true REI value), with a confidence level of approximately 68%. CONCLUSIONS: We have developed and evaluated our method using original clinical registrations without generating any synthetic/simulated data. Moreover, test data were acquired from a different environment than that of training data, so that the method was validated robustly. The results of this study showed that our algorithm performs reasonably well in challenging scenarios.

In Silico Approach for the Definition of radiomiRNomic Signatures for Breast Cancer Differential Diagnosis

  • Gallivanone, F.
  • Cava, C.
  • Corsi, F.
  • Bertoli, G.
  • Castiglioni, I.
Int J Mol Sci 2019 Journal Article, cited 2 times
Website
Personalized medicine relies on the integration and consideration of specific characteristics of the patient, such as tumor phenotypic and genotypic profiling. BACKGROUND: Radiogenomics aim to integrate phenotypes from tumor imaging data with genomic data to discover genetic mechanisms underlying tumor development and phenotype. METHODS: We describe a computational approach that correlates phenotype from magnetic resonance imaging (MRI) of breast cancer (BC) lesions with microRNAs (miRNAs), mRNAs, and regulatory networks, developing a radiomiRNomic map. We validated our approach to the relationships between MRI and miRNA expression data derived from BC patients. We obtained 16 radiomic features quantifying the tumor phenotype. We integrated the features with miRNAs regulating a network of pathways specific for a distinct BC subtype. RESULTS: We found six miRNAs correlated with imaging features in Luminal A (miR-1537, -205, -335, -337, -452, and -99a), seven miRNAs (miR-142, -155, -190, -190b, -1910, -3617, and -429) in HER2+, and two miRNAs (miR-135b and -365-2) in Basal subtype. We demonstrate that the combination of correlated miRNAs and imaging features have better classification power of Luminal A versus the different BC subtypes than using miRNAs or imaging alone. CONCLUSION: Our computational approach could be used to identify new radiomiRNomic profiles of multi-omics biomarkers for BC differential diagnosis and prognosis.

Extraction of pulmonary vessels and tumour from plain computed tomography sequence

  • Ganapathy, Sridevi
  • Ashar, Kinnari
  • Kathirvelu, D
2018 Conference Proceedings, cited 0 times
Website

Performance analysis for nonlinear tomographic data processing

  • Gang, Grace J
  • Guo, Xueqi
  • Stayman IV, J Webster
2019 Conference Proceedings, cited 0 times
Website

Improving the Subtype Classification of Non-small Cell Lung Cancer by Elastic Deformation Based Machine Learning

  • Gao, Yang
  • Song, Fan
  • Zhang, Peng
  • Liu, Jian
  • Cui, Jingjing
  • Ma, Yingying
  • Zhang, Guanglei
  • Luo, Jianwen
J Digit Imaging 2021 Journal Article, cited 0 times
Website
Non-invasive image-based machine learning models have been used to classify subtypes of non-small cell lung cancer (NSCLC). However, the classification performance is limited by the dataset size, because insufficient data cannot fully represent the characteristics of the tumor lesions. In this work, a data augmentation method named elastic deformation is proposed to artificially enlarge the image dataset of NSCLC patients with two subtypes (squamous cell carcinoma and large cell carcinoma) of 3158 images. Elastic deformation effectively expanded the dataset by generating new images, in which tumor lesions go through elastic shape transformation. To evaluate the proposed method, two classification models were trained on the original and augmented dataset, respectively. Using augmented dataset for training significantly increased classification metrics including area under the curve (AUC) values of receiver operating characteristics (ROC) curves, accuracy, sensitivity, specificity, and f1-score, thus improved the NSCLC subtype classification performance. These results suggest that elastic deformation could be an effective data augmentation method for NSCLC tumor lesion images, and building classification models with the help of elastic deformation has the potential to serve for clinical lung cancer diagnosis and treatment design.

Simultaneous emission and attenuation reconstruction in time-of-flight PET using a reference object

  • Garcia-Perez, P.
  • Espana, S.
EJNMMI Phys 2020 Journal Article, cited 0 times
Website
BACKGROUND: Simultaneous reconstruction of emission and attenuation images in time-of-flight (TOF) positron emission tomography (PET) does not provide a unique solution. In this study, we propose to solve this limitation by including additional information given by a reference object with known attenuation placed outside the patient. Different configurations of the reference object were studied including geometry, material composition, and activity, and an optimal configuration was defined. In addition, this configuration was tested for different timing resolutions and noise levels. RESULTS: The proposed strategy was tested in 2D simulations obtained by forward projection of available PET/CT data and noise was included using Monte Carlo techniques. Obtained results suggest that the optimal configuration corresponds to a water cylinder inserted in the patient table and filled with activity. In that case, mean differences between reconstructed and true images were below 10%. However, better results can be obtained by increasing the activity of the reference object. CONCLUSION: This study shows promising results that might allow to obtain an accurate attenuation map from pure TOF-PET data without prior knowledge obtained from CT, MRI, or transmission scans.

An Improved Mammogram Classification Approach Using Back Propagation Neural Network

  • Gautam, Aman
  • Bhateja, Vikrant
  • Tiwari, Ananya
  • Satapathy, Suresh Chandra
2017 Book Section, cited 16 times
Website
Mammograms are generally contaminated by quantum noise, degrading their visual quality and thereby the performance of the classifier in Computer-Aided Diagnosis (CAD). Hence, enhancement of mammograms is necessary to improve the visual quality and detectability of the anomalies present in the breasts. In this paper, a sigmoid based non-linear function has been applied for contrast enhancement of mammograms. The enhanced mammograms are used to define the texture of the detected anomaly using Gray Level Co-occurrence Matrix (GLCM) features. Later, a Back Propagation Artificial Neural Network (BP-ANN) is used as a classification tool for segregating the mammogram into abnormal or normal. The proposed classifier approach has reported to be the one with considerably better accuracy in comparison to other existing approaches.

A resource for the assessment of lung nodule size estimation methods: database of thoracic CT scans of an anthropomorphic phantom

  • Gavrielides, Marios A
  • Kinnard, Lisa M
  • Myers, Kyle J
  • Peregoy, Jennifer
  • Pritchard, William F
  • Zeng, Rongping
  • Esparza, Juan
  • Karanian, John
  • Petrick, Nicholas
Optics express 2010 Journal Article, cited 50 times
Website
A number of interrelated factors can affect the precision and accuracy of lung nodule size estimation. To quantify the effect of these factors, we have been conducting phantom CT studies using an anthropomorphic thoracic phantom containing a vasculature insert to which synthetic nodules were inserted or attached. Ten repeat scans were acquired on different multi-detector scanners, using several sets of acquisition and reconstruction protocols and various nodule characteristics (size, shape, density, location). This study design enables both bias and variance analysis for the nodule size estimation task. The resulting database is in the process of becoming publicly available as a resource to facilitate the assessment of lung nodule size estimation methodologies and to enable comparisons between different methods regarding measurement error. This resource complements public databases of clinical data and will contribute towards the development of procedures that will maximize the utility of CT imaging for lung cancer screening and tumor therapy evaluation.

Benefit of overlapping reconstruction for improving the quantitative assessment of CT lung nodule volume

  • Gavrielides, Marios A
  • Zeng, Rongping
  • Myers, Kyle J
  • Sahiner, Berkman
  • Petrick, Nicholas
Academic Radiology 2013 Journal Article, cited 23 times
Website
RATIONALE AND OBJECTIVES: The aim of this study was to quantify the effect of overlapping reconstruction on the precision and accuracy of lung nodule volume estimates in a phantom computed tomographic (CT) study. MATERIALS AND METHODS: An anthropomorphic phantom was used with a vasculature insert on which synthetic lung nodules were attached. Repeated scans of the phantom were acquired using a 64-slice CT scanner. Overlapping and contiguous reconstructions were performed for a range of CT imaging parameters (exposure, slice thickness, pitch, reconstruction kernel) and a range of nodule characteristics (size, density). Nodule volume was estimated with a previously developed matched-filter algorithm. RESULTS: Absolute percentage bias across all nodule sizes (n = 2880) was significantly lower when overlapping reconstruction was used, with an absolute percentage bias of 6.6% (95% confidence interval [CI], 6.4-6.9), compared to 13.2% (95% CI, 12.7-13.8) for contiguous reconstruction. Overlapping reconstruction also showed a precision benefit, with a lower standard percentage error of 7.1% (95% CI, 6.9-7.2) compared with 15.3% (95% CI, 14.9-15.7) for contiguous reconstructions across all nodules. Both effects were more pronounced for the smaller, subcentimeter nodules. CONCLUSIONS: These results support the use of overlapping reconstruction to improve the quantitative assessment of nodule size with CT imaging.

Automatic Segmentation of Colon in 3D CT Images and Removal of Opacified Fluid Using Cascade Feed Forward Neural Network

  • Gayathri Devi, K
  • Radhakrishnan, R
Computational and Mathematical Methods in Medicine 2015 Journal Article, cited 5 times
Website

Segmentation of colon and removal of opacified fluid for virtual colonoscopy

  • Gayathri, Devi K
  • Radhakrishnan, R
  • Rajamani, Kumar
Pattern Analysis and Applications 2017 Journal Article, cited 0 times
Website
Colorectal cancer (CRC) is the third most common type of cancer. The use of techniques such as flexible sigmoidoscopy and capsule endoscopy for the screening of colorectal cancer causes physical pain and hardship to the patients. Hence, to overcome the above disadvantages, computed tomography (CT) can be employed for the identification of polyps or growth, while screening for CRC. This proposed approach was implemented to improve the accuracy and to reduce the computation time of the accurate segmentation of the colon segments from the abdominal CT images which contain anatomical organs such as lungs, small bowels, large bowels (Colon), ribs, opacified fluid and bones. The segmentation is performed in two major steps. The first step segments the air-filled colon portions by placing suitable seed points using modified 3D seeded region growing which identify and match the similar voxels by 6-neighborhood connectivity technique. The segmentation of the opacified fluid portions is done using fuzzy connectedness approach enhanced with interval thresholding. The membership classes are defined and the voxels are categorized based on the class value. Interval thresholding is performed so that the bones and opacified fluid parts may be extracted. The bones are removed by the placement of seed points as the existence of the continuity of the bone region is more in the axial slices. The resultant image containing bones is subtracted from the threshold output to segment the opacified fluid segments in all the axial slices of a dataset. Finally, concatenation of the opacified fluid with the segmented colon is performed for the 3D rendering of the segmented colon. This method was implemented in 15 datasets downloaded from TCIA and in real-time dataset in both supine and prone position and the accuracy achieved was 98.73%.

Machine Learning Methods for Image Analysis in Medical Applications From Alzheimer’s Disease, Brain Tumors, to Assisted Living

  • Chenjie Ge
2020 Thesis, cited 0 times
Website
Healthcare has progressed greatly nowadays owing to technological advances, where machine learning plays an important role in processing and analyzing a large amount of medical data. This thesis investigates four healthcare-related issues (Alzheimer's disease detection, glioma classification, human fall detection, and obstacle avoidance in prosthetic vision), where the underlying methodologies are associated with machine learning and computer vision. For Alzheimer’s disease (AD) diagnosis, apart from symptoms of patients, Magnetic Resonance Images (MRIs) also play an important role. Inspired by the success of deep learning, a new multi-stream multi-scale Convolutional Neural Network (CNN) architecture is proposed for AD detection from MRIs, where AD features are characterized in both the tissue level and the scale level for improved feature learning. Good classification performance is obtained for AD/NC (normal control) classification with test accuracy 94.74%. In glioma subtype classification, biopsies are usually needed for determining different molecular-based glioma subtypes. We investigate non-invasive glioma subtype prediction from MRIs by using deep learning. A 2D multi-stream CNN architecture is used to learn the features of gliomas from multi-modal MRIs, where the training dataset is enlarged with synthetic brain MRIs generated by pairwise Generative Adversarial Networks (GANs). Test accuracy 88.82% has been achieved for IDH mutation (a molecular-based subtype) prediction. A new deep semi-supervised learning method is also proposed to tackle the problem of missing molecular-related labels in training datasets for improving the performance of glioma classification. In other two applications, we also address video-based human fall detection by using co-saliency-enhanced Recurrent Convolutional Networks (RCNs), as well as obstacle avoidance in prosthetic vision by characterizing obstacle-related video features using a Spiking Neural Network (SNN). These investigations can benefit future research, where artificial intelligence/deep learning may open a new way for real medical applications.

SDCT-AuxNet(theta): DCT augmented stain deconvolutional CNN with auxiliary classifier for cancer diagnosis

  • Gehlot, Shiv
  • Gupta, Anubha
  • Gupta, Ritu
Medical Image Analysis 2020 Journal Article, cited 6 times
Website
Acute lymphoblastic leukemia (ALL) is a pervasive pediatric white blood cell cancer across the globe. With the popularity of convolutional neural networks (CNNs), computer-aided diagnosis of cancer has attracted considerable attention. Such tools are easily deployable and are cost-effective. Hence, these can enable extensive coverage of cancer diagnostic facilities. However, the development of such a tool for ALL cancer was challenging so far due to the non-availability of a large training dataset. The visual similarity between the malignant and normal cells adds to the complexity of the problem. This paper discusses the recent release of a large dataset and presents a novel deep learning architecture for the classification of cell images of ALL cancer. The proposed architecture, namely, SDCT-AuxNet(theta) is a 2-module framework that utilizes a compact CNN as the main classifier in one module and a Kernel SVM as the auxiliary classifier in the other one. While CNN classifier uses features through bilinear-pooling, spectral-averaged features are used by the auxiliary classifier. Further, this CNN is trained on the stain deconvolved quantity images in the optical density domain instead of the conventional RGB images. A novel test strategy is proposed that exploits both the classifiers for decision making using the confidence scores of their predicted class labels. Elaborate experiments have been carried out on our recently released public dataset of 15114 images of ALL cancer and healthy cells to establish the validity of the proposed methodology that is also robust to subject-level variability. A weighted F1 score of 94.8% is obtained that is best so far on this challenging dataset.

A CNN-based unified framework utilizing projection loss in unison with label noise handling for multiple Myeloma cancer diagnosis

  • Gehlot, S.
  • Gupta, A.
  • Gupta, R.
Med Image Anal 2021 Journal Article, cited 0 times
Website
Multiple Myeloma (MM) is a malignancy of plasma cells. Similar to other forms of cancer, it demands prompt diagnosis for reducing the risk of mortality. The conventional diagnostic tools are resource-intense and hence, these solutions are not easily scalable for extending their reach to the masses. Advancements in deep learning have led to rapid developments in affordable, resource optimized, easily deployable computer-assisted solutions. This work proposes a unified framework for MM diagnosis using microscopic blood cell imaging data that addresses the key challenges of inter-class visual similarity of healthy versus cancer cells and that of the label noise of the dataset. To extract class distinctive features, we propose projection loss to maximize the projection of a sample's activation on the respective class vector besides imposing orthogonality constraints on the class vectors. This projection loss is used along with the cross-entropy loss to design a dual branch architecture that helps achieve improved performance and provides scope for targeting the label noise problem. Based on this architecture, two methodologies have been proposed to correct the noisy labels. A coupling classifier has also been proposed to resolve the conflicts in the dual-branch architecture's predictions. We have utilized a large dataset of 72 subjects (26 healthy and 46 MM cancer) containing a total of 74996 images (including 34555 training cell images and 40441 test cell images). This is so far the most extensive dataset on Multiple Myeloma cancer ever reported in the literature. An ablation study has also been carried out. The proposed architecture performs best with a balanced accuracy of 94.17% on binary cell classification of healthy versus cancer in the comparative performance with ten state-of-the-art architectures. Extensive experiments on two additional publicly available datasets of two different modalities have also been utilized for analyzing the label noise handling capability of the proposed methodology. The code will be available under https://github.com/shivgahlout/CAD-MM.

Ultra-Fast 3D GPGPU Region Extractions for Anatomy Segmentation

  • George, Jose
  • Mysoon, N. S.
  • Antony, Nixima
2019 Conference Paper, cited 0 times
Website
Region extractions are ubiquitous in any anatomy segmentation. Region growing is one such method. Starting from an initial seed point, it grows a region of interest until all valid voxels are checked, thereby resulting in an object segmentation. Although widely used, it is computationally expensive because of its sequential approach. In this paper, we present a parallel and high performance alternate for region growing using GPGPU capability. The idea is to approximate region growing requirements within an algorithm using a parallel connected-component labeling (CCL) solution. To showcase this, we selected a typical lung segmentation problem using region growing. In CPU, sequential approach consists of 3D region growing inside a mask, that is created after applying a threshold. In GPU, parallel alternative is to apply parallel CCL and select the biggest region of interest. We evaluated our approach on 45 clinical chest CT scans in LIDC data from TCIA repository. With respect to CPU, our CUDA based GPU facilitated an average performance improvement of 240× approximately. Speed up is so profound that it can be even applied to 4D lung segmentation at 6 fps.

Synthetic Head and Neck and Phantom Images for Determining Deformable Image Registration Accuracy in Magnetic Resonance Imaging

  • Ger, Rachel B
  • Yang, Jinzhong
  • Ding, Yao
  • Jacobsen, Megan C
  • Cardenas, Carlos E
  • Fuller, Clifton D
  • Howell, Rebecca M
  • Li, Heng
  • Stafford, R Jason
  • Zhou, Shouhao
Medical Physics 2018 Journal Article, cited 0 times
Website

Radiomics features of the primary tumor fail to improve prediction of overall survival in large cohorts of CT- and PET-imaged head and neck cancer patients

  • Ger, Rachel B
  • Zhou, Shouhao
  • Elgohari, Baher
  • Elhalawani, Hesham
  • Mackin, Dennis M
  • Meier, Joseph G
  • Nguyen, Callistus M
  • Anderson, Brian M
  • Gay, Casey
  • Ning, Jing
  • Fuller, Clifton D
  • Li, Heng
  • Howell, Rebecca M
  • Layman, Rick R
  • Mawlawi, Osama
  • Stafford, R Jason
  • Aerts, Hugo JWL
  • Court, Laurence E.
PLoS One 2019 Journal Article, cited 0 times
Website
Radiomics studies require many patients in order to power them, thus patients are often combined from different institutions and using different imaging protocols. Various studies have shown that imaging protocols affect radiomics feature values. We examined whether using data from cohorts with controlled imaging protocols improved patient outcome models. We retrospectively reviewed 726 CT and 686 PET images from head and neck cancer patients, who were divided into training or independent testing cohorts. For each patient, radiomics features with different preprocessing were calculated and two clinical variables-HPV status and tumor volume-were also included. A Cox proportional hazards model was built on the training data by using bootstrapped Lasso regression to predict overall survival. The effect of controlled imaging protocols on model performance was evaluated by subsetting the original training and independent testing cohorts to include only patients whose images were obtained using the same imaging protocol and vendor. Tumor volume, HPV status, and two radiomics covariates were selected for the CT model, resulting in an AUC of 0.72. However, volume alone produced a higher AUC, whereas adding radiomics features reduced the AUC. HPV status and one radiomics feature were selected as covariates for the PET model, resulting in an AUC of 0.59, but neither covariate was significantly associated with survival. Limiting the training and independent testing to patients with the same imaging protocol reduced the AUC for CT patients to 0.55, and no covariates were selected for PET patients. Radiomics features were not consistently associated with survival in CT or PET images of head and neck patients, even within patients with the same imaging protocol.

Glioblastoma Multiforme: Exploratory Radiogenomic Analysis by Using Quantitative Image Features

  • Gevaert, Olivier
  • Mitchell, Lex A
  • Achrol, Achal S
  • Xu, Jiajing
  • Echegaray, Sebastian
  • Steinberg, Gary K
  • Cheshier, Samuel H
  • Napel, Sandy
  • Zaharchuk, Greg
  • Plevritis, Sylvia K
RadiologyRadiology 2014 Journal Article, cited 151 times
Website
Purpose: To derive quantitative image features from magnetic resonance (MR) images that characterize the radiographic phenotype of glioblastoma multiforme (GBM) lesions and to create radiogenomic maps associating these features with various molecular data. Materials and Methods: Clinical, molecular, and MR imaging data for GBMs in 55 patients were obtained from the Cancer Genome Atlas and the Cancer Imaging Archive after local ethics committee and institutional review board approval. Regions of interest (ROIs) corresponding to enhancing necrotic portions of tumor and peritumoral edema were drawn, and quantitative image features were derived from these ROIs. Robust quantitative image features were defined on the basis of an intraclass correlation coefficient of 0.6 for a digital algorithmic modification and a test-retest analysis. The robust features were visualized by using hierarchic clustering and were correlated with survival by using Cox proportional hazards modeling. Next, these robust image features were correlated with manual radiologist annotations from the Visually Accessible Rembrandt Images (VASARI) feature set and GBM molecular subgroups by using nonparametric statistical tests. A bioinformatic algorithm was used to create gene expression modules, defined as a set of coexpressed genes together with a multivariate model of cancer driver genes predictive of the module's expression pattern. Modules were correlated with robust image features by using the Spearman correlation test to create radiogenomic maps and to link robust image features with molecular pathways. Results: Eighteen image features passed the robustness analysis and were further analyzed for the three types of ROIs, for a total of 54 image features. Three enhancement features were significantly correlated with survival, 77 significant correlations were found between robust quantitative features and the VASARI feature set, and seven image features were correlated with molecular subgroups (P < .05 for all). A radiogenomics map was created to link image features with gene expression modules and allowed linkage of 56% (30 of 54) of the image features with biologic processes. Conclusion: Radiogenomic approaches in GBM have the potential to predict clinical and molecular characteristics of tumors noninvasively.

Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes

  • Gevaert, O.
  • Nabian, M.
  • Bakr, S.
  • Everaert, C.
  • Shinde, J.
  • Manukyan, A.
  • Liefeld, T.
  • Tabor, T.
  • Xu, J.
  • Lupberger, J.
  • Haas, B. J.
  • Baumert, T. F.
  • Hernaez, M.
  • Reich, M.
  • Quintana, F. J.
  • Uhlmann, E. J.
  • Krichevsky, A. M.
  • Mesirov, J. P.
  • Carey, V.
  • Pochet, N.
JCO Clin Cancer Inform 2020 Journal Article, cited 1 times
Website
PURPOSE: The availability of increasing volumes of multiomics, imaging, and clinical data in complex diseases such as cancer opens opportunities for the formulation and development of computational imaging genomics methods that can link multiomics, imaging, and clinical data. METHODS: Here, we present the Imaging-AMARETTO algorithms and software tools to systematically interrogate regulatory networks derived from multiomics data within and across related patient studies for their relevance to radiography and histopathology imaging features predicting clinical outcomes. RESULTS: To demonstrate its utility, we applied Imaging-AMARETTO to integrate three patient studies of brain tumors, specifically, multiomics with radiography imaging data from The Cancer Genome Atlas (TCGA) glioblastoma multiforme (GBM) and low-grade glioma (LGG) cohorts and transcriptomics with histopathology imaging data from the Ivy Glioblastoma Atlas Project (IvyGAP) GBM cohort. Our results show that Imaging-AMARETTO recapitulates known key drivers of tumor-associated microglia and macrophage mechanisms, mediated by STAT3, AHR, and CCR2, and neurodevelopmental and stemness mechanisms, mediated by OLIG2. Imaging-AMARETTO provides interpretation of their underlying molecular mechanisms in light of imaging biomarkers of clinical outcomes and uncovers novel master drivers, THBS1 and MAP2, that establish relationships across these distinct mechanisms. CONCLUSION: Our network-based imaging genomics tools serve as hypothesis generators that facilitate the interrogation of known and uncovering of novel hypotheses for follow-up with experimental validation studies. We anticipate that our Imaging-AMARETTO imaging genomics tools will be useful to the community of biomedical researchers for applications to similar studies of cancer and other complex diseases with available multiomics, imaging, and clinical data.

Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results

  • Gevaert, Olivier
  • Xu, Jiajing
  • Hoang, Chuong D
  • Leung, Ann N
  • Xu, Yue
  • Quon, Andrew
  • Rubin, Daniel L
  • Napel, Sandy
  • Plevritis, Sylvia K
RadiologyRadiology 2012 Journal Article, cited 187 times
Website
PURPOSE: To identify prognostic imaging biomarkers in non-small cell lung cancer (NSCLC) by means of a radiogenomics strategy that integrates gene expression and medical images in patients for whom survival outcomes are not available by leveraging survival data in public gene expression data sets. MATERIALS AND METHODS: A radiogenomics strategy for associating image features with clusters of coexpressed genes (metagenes) was defined. First, a radiogenomics correlation map is created for a pairwise association between image features and metagenes. Next, predictive models of metagenes are built in terms of image features by using sparse linear regression. Similarly, predictive models of image features are built in terms of metagenes. Finally, the prognostic significance of the predicted image features are evaluated in a public gene expression data set with survival outcomes. This radiogenomics strategy was applied to a cohort of 26 patients with NSCLC for whom gene expression and 180 image features from computed tomography (CT) and positron emission tomography (PET)/CT were available. RESULTS: There were 243 statistically significant pairwise correlations between image features and metagenes of NSCLC. Metagenes were predicted in terms of image features with an accuracy of 59%-83%. One hundred fourteen of 180 CT image features and the PET standardized uptake value were predicted in terms of metagenes with an accuracy of 65%-86%. When the predicted image features were mapped to a public gene expression data set with survival outcomes, tumor size, edge shape, and sharpness ranked highest for prognostic significance. CONCLUSION: This radiogenomics strategy for identifying imaging biomarkers may enable a more rapid evaluation of novel imaging modalities, thereby accelerating their translation to personalized medicine.

T2-FDL: A robust sparse representation method using adaptive type-2 fuzzy dictionary learning for medical image classification

  • Ghasemi, Majid
  • Kelarestaghi, Manoochehr
  • Eshghi, Farshad
  • Sharifi, Arash
Expert Systems with Applications 2020 Journal Article, cited 0 times
Website
In this paper, a robust sparse representation for medical image classification is proposed based on the adaptive type-2 fuzzy learning (T2-FDL) system. In the proposed method, sparse coding and dictionary learning processes are executed iteratively until a near-optimal dictionary is obtained. The sparse coding step aiming at finding a combination of dictionary atoms to represent the input data efficiently, and the dictionary learning step rigorously adjusts a minimum set of dictionary items. The two-step operation helps create an adaptive sparse representation algorithm by involving the type-2 fuzzy sets in the design process of image classification. Since the existing image measurements are not made under the same conditions and with the same accuracy, the performance of medical diagnosis is always affected by noise and uncertainty. By introducing an adaptive type-2 fuzzy learning method, a better approximation in an environment with higher degrees of uncertainty and noise is achieved. The experiments are executed over two open-access brain tumor magnetic resonance image databases, REMBRANDT and TCGA-LGG, from The Cancer Imaging Archive (TCIA). The experimental results of a brain tumor classification task show that the proposed T2-FDL method can adequately minimize the negative effects of uncertainty in the input images. The results demonstrate the outperformance of T2-FDL compared to other important classification methods in the literature, in terms of accuracy, specificity, and sensitivity.

Medical Imaging Segmentation Assessment via Bayesian Approaches to Fusion, Accuracy and Variability Estimation with Application to Head and Neck Cancer

  • Ghattas, Andrew Emile
2017 Thesis, cited 0 times
Website

Deep Learning for Low-Dose CT Denoising Using Perceptual Loss and Edge Detection Layer

  • Gholizadeh-Ansari, M.
  • Alirezaie, J.
  • Babyn, P.
J Digit Imaging 2019 Journal Article, cited 1 times
Website
Low-dose CT denoising is a challenging task that has been studied by many researchers. Some studies have used deep neural networks to improve the quality of low-dose CT images and achieved fruitful results. In this paper, we propose a deep neural network that uses dilated convolutions with different dilation rates instead of standard convolution helping to capture more contextual information in fewer layers. Also, we have employed residual learning by creating shortcut connections to transmit image information from the early layers to later ones. To further improve the performance of the network, we have introduced a non-trainable edge detection layer that extracts edges in horizontal, vertical, and diagonal directions. Finally, we demonstrate that optimizing the network by a combination of mean-square error loss and perceptual loss preserves many structural details in the CT image. This objective function does not suffer from over smoothing and blurring effects causing by per-pixel loss and grid-like artifacts resulting from perceptual loss. The experiments show that each modification to the network improves the outcome while changing the complexity of the network, minimally.

Brain tumor detection from MRI image: An approach

  • Ghosh, Debjyoti
  • Bandyopadhyay, Samir Kumar
International Journal of Applied Research 2017 Journal Article, cited 0 times
Website
A brain tumor is an abnormal growth of cells within the brain, which can be cancerous or noncancerous (benign). This paper detects different types of tumors and cancerous growth within the brain and other associated areas within the brain by using computerized methods on MRI images of a patient. It is also possible to track the growth patterns of such tumors.

Tumor Segmentation in Brain MRI: U-Nets versus Feature Pyramid Network

  • Ghosh, Sourodip
  • Santosh, K.C.
2021 Conference Paper, cited 0 times
Website
Manifestations of brain tumors can trigger various psychiatric symptoms. Brain tumor detection can efficiently solve or reduce chances of occurrences of diseases, such as Alzheimer's disease, dementia-based disorders, multiple sclerosis and bipolar disorder. In this paper, we propose a segmentation-based approach to detect brain tumors in MRI 1 1 . We provide a comparative study between two different U-Net architectures (U-Net: baseline and U-Net: ResNeXt50 backbone) and a Feature Pyramid Network (FPN) that are trained/validated on the TCGA-LGG dataset of size 3, 929 images. U-Net architecture with ResNeXt50 backbone achieves the best Dice coefficient of 0.932, while baseline U-Net and FPN separately achieve Dice coefficients of 0.846 and 0.899, respectively. The results obtained from U-Net with ResNeXt50 backbone outperform previous works.

Role of Imaging in the Era of Precision Medicine

  • Giardino, Angela
  • Gupta, Supriya
  • Olson, Emmi
  • Sepulveda, Karla
  • Lenchik, Leon
  • Ivanidze, Jana
  • Rakow-Penner, Rebecca
  • Patel, Midhir J
  • Subramaniam, Rathan M
  • Ganeshan, Dhakshinamoorthy
Academic Radiology 2017 Journal Article, cited 12 times
Website
Precision medicine is an emerging approach for treating medical disorders, which takes into account individual variability in genetic and environmental factors. Preventive or therapeutic interventions can then be directed to those who will benefit most from targeted interventions, thereby maximizing benefits and minimizing costs and complications. Precision medicine is gaining increasing recognition by clinicians, healthcare systems, pharmaceutical companies, patients, and the government. Imaging plays a critical role in precision medicine including screening, early diagnosis, guiding treatment, evaluating response to therapy, and assessing likelihood of disease recurrence. The Association of University Radiologists Radiology Research Alliance Precision Imaging Task Force convened to explore the current and future role of imaging in the era of precision medicine and summarized its finding in this article. We review the increasingly important role of imaging in various oncological and non-oncological disorders. We also highlight the challenges for radiology in the era of precision medicine.

Automatic Multi-organ Segmentation on Abdominal CT with Dense V-networks

  • E. Gibson
  • F. Giganti
  • Y. Hu
  • E. Bonmati
  • S. Bandula
  • K. Gurusamy
  • B. Davidson
  • S. P. Pereira
  • M. J. Clarkson
  • D. C. Barratt
IEEE Transactions on Medical Imaging 2018 Journal Article, cited 14 times
Website

Towards Image-Guided Pancreas and Biliary Endoscopy: Automatic Multi-organ Segmentation on Abdominal CT with Dense Dilated Networks

  • Gibson, Eli
  • Giganti, Francesco
  • Hu, Yipeng
  • Bonmati, Ester
  • Bandula, Steve
  • Gurusamy, Kurinchi
  • Davidson, Brian R
  • Pereira, Stephen P
  • Clarkson, Matthew J
  • Barratt, Dean C
2017 Conference Proceedings, cited 14 times
Website

Quantitative CT assessment of emphysema and airways in relation to lung cancer risk

  • Gierada, David S
  • Guniganti, Preethi
  • Newman, Blake J
  • Dransfield, Mark T
  • Kvale, Paul A
  • Lynch, David A
  • Pilgram, Thomas K
RadiologyRadiology 2011 Journal Article, cited 41 times
Website

Projected outcomes using different nodule sizes to define a positive CT lung cancer screening examination

  • Gierada, David S
  • Pinsky, Paul
  • Nath, Hrudaya
  • Chiles, Caroline
  • Duan, Fenghai
  • Aberle, Denise R
2014 Journal Article, cited 74 times
Website
Background Computed tomography (CT) screening for lung cancer has been associated with a high frequency of false positive results because of the high prevalence of indeterminate but usually benign small pulmonary nodules. The acceptability of reducing false-positive rates and diagnostic evaluations by increasing the nodule size threshold for a positive screen depends on the projected balance between benefits and risks. Methods We examined data from the National Lung Screening Trial (NLST) to estimate screening CT performance and outcomes for scans with nodules above the 4 mm NLST threshold used to classify a CT screen as positive. Outcomes assessed included screening results, subsequent diagnostic tests performed, lung cancer histology and stage distribution, and lung cancer mortality. Sensitivity, specificity, positive predictive value, and negative predictive value were calculated for the different nodule size thresholds. All statistical tests were two-sided. Results In 64% of positive screens (11 598/18 141), the largest nodule was 7 mm or less in greatest transverse diameter. By increasing the threshold, the percentages of lung cancer diagnoses that would have been missed or delayed and false positives that would have been avoided progressively increased, for example from 1.0% and 15.8% at a 5 mm threshold to 10.5% and 65.8% at an 8 mm threshold, respectively. The projected reductions in postscreening follow-up CT scans and invasive procedures also increased as the threshold was raised. Differences across nodules sizes for lung cancer histology and stage distribution were small but statistically significant. There were no differences across nodule sizes in survival or mortality. Conclusion Raising the nodule size threshold for a positive screen would substantially reduce false-positive CT screenings and medical resource utilization with a variable impact on screening outcomes.

Vessel extraction from breast MR

  • Gierlinger, Marco
  • Brandner, Dinah
  • Zagar, Bernhard G.
2021 Conference Proceedings, cited 0 times
We present an extension of the previous work, where a multi-seed region growing algorithm was shown, that extracts segments from breast MRI. The algorithm of our extended work filters elongated segments from the segments derived by the MSRG algorithm to obtain vessel-like structures. This filter is a skeletonization-like algorithm that collects useful information about the segments' thickness, length, etc. A model is shown that scans through the solution space of the MSRG algorithm by adjusting its parameters and by providing shape information for the filter. We further elaborate on the usefulness of the algorithm to assist medical experts in their daignosis of diseases relevant to angiography.

Machine Learning in Medical Imaging

  • Giger, M. L.
J Am Coll Radiol 2018 Journal Article, cited 157 times
Website
Advances in both imaging and computers have synergistically led to a rapid rise in the potential use of artificial intelligence in various radiological imaging tasks, such as risk assessment, detection, diagnosis, prognosis, and therapy response, as well as in multi-omics disease discovery. A brief overview of the field is given here, allowing the reader to recognize the terminology, the various subfields, and components of machine learning, as well as the clinical potential. Radiomics, an expansion of computer-aided diagnosis, has been defined as the conversion of images to minable data. The ultimate benefit of quantitative radiomics is to (1) yield predictive image-based phenotypes of disease for precision medicine or (2) yield quantitative image-based phenotypes for data mining with other -omics for discovery (ie, imaging genomics). For deep learning in radiology to succeed, note that well-annotated large data sets are needed since deep networks are complex, computer software and hardware are evolving constantly, and subtle differences in disease states are more difficult to perceive than differences in everyday objects. In the future, machine learning in radiology is expected to have a substantial clinical impact with imaging examinations being routinely obtained in clinical practice, providing an opportunity to improve decision support in medical image interpretation. The term of note is decision support, indicating that computers will augment human decision making, making it more effective and efficient. The clinical impact of having computers in the routine clinical practice may allow radiologists to further integrate their knowledge with their clinical colleagues in other medical specialties and allow for precision medicine.

Radiomics: Images are more than pictures, they are data

  • Gillies, Robert J
  • Kinahan, Paul E
  • Hricak, Hedvig
RadiologyRadiology 2015 Journal Article, cited 694 times
Website

Intuitive Error Space Exploration of Medical Image Data in Clinical Daily Routine

  • Gillmann, Christina
  • Arbeláez, Pablo
  • Peñaloza, José Tiberio Hernández
  • Hagen, Hans
  • Wischgoll, Thomas
2017 Conference Paper, cited 3 times
Website

An Uncertainty-aware Workflow for Keyhole Surgery Planning using Hierarchical Image Semantics

  • Gillmann, Christina
  • Maack, Robin G. C.
  • Post, Tobias
  • Wischgoll, Thomas
  • Hagen, Hans
Visual Informatics 2018 Journal Article, cited 1 times
Website
Keyhole surgeries become increasingly important in clinical daily routine as they help minimizing the damage of a patient’s healthy tissue. The planning of keyhole surgeries is based on medical imaging and an important factor that influences the surgeries’ success. Due to the image reconstruction process, medical image data contains uncertainty that exacerbates the planning of a keyhole surgery. In this paper we present a visual workflow that helps clinicians to examine and compare different surgery paths as well as visualizing the patients’ affected tissue. The analysis is based on the concept of hierarchical image semantics, that segment the underlying image data with respect to the input images’ uncertainty and the users understanding of tissue composition. Users can define arbitrary surgery paths that they need to investigate further. The defined paths can be queried by a rating function to identify paths that fulfill user-defined properties. The workflow allows a visual inspection of the affected tissues and its substructures. Therefore, the workflow includes a linked view system indicating the three-dimensional location of selected surgery paths as well as how these paths affect the patients tissue. To show the effectiveness of the presented approach, we applied it to the planning of a keyhole surgery of a brain tumor removal and a kneecap surgery.

Interpretable Machine Learning Model for Locoregional Relapse Prediction in Oropharyngeal Cancers

  • Giraud, Paul
  • Giraud, Philippe
  • Nicolas, Eliot
  • Boisselier, Pierre
  • Alfonsi, Marc
  • Rives, Michel
  • Bardet, Etienne
  • Calugaru, Valentin
  • Noel, Georges
  • Chajon, Enrique
Cancers 2021 Journal Article, cited 0 times
Website

Planning, guidance, and quality assurance of pelvic screw placement using deformable image registration

  • Goerres, J.
  • Uneri, A.
  • Jacobson, M.
  • Ramsay, B.
  • De Silva, T.
  • Ketcha, M.
  • Han, R.
  • Manbachi, A.
  • Vogt, S.
  • Kleinszig, G.
  • Wolinsky, J. P.
  • Osgood, G.
  • Siewerdsen, J. H.
Phys Med Biol 2017 Journal Article, cited 4 times
Website
Percutaneous pelvic screw placement is challenging due to narrow bone corridors surrounded by vulnerable structures and difficult visual interpretation of complex anatomical shapes in 2D x-ray projection images. To address these challenges, a system for planning, guidance, and quality assurance (QA) is presented, providing functionality analogous to surgical navigation, but based on robust 3D-2D image registration techniques using fluoroscopy images already acquired in routine workflow. Two novel aspects of the system are investigated: automatic planning of pelvic screw trajectories and the ability to account for deformation of surgical devices (K-wire deflection). Atlas-based registration is used to calculate a patient-specific plan of screw trajectories in preoperative CT. 3D-2D registration aligns the patient to CT within the projective geometry of intraoperative fluoroscopy. Deformable known-component registration (dKC-Reg) localizes the surgical device, and the combination of plan and device location is used to provide guidance and QA. A leave-one-out analysis evaluated the accuracy of automatic planning, and a cadaver experiment compared the accuracy of dKC-Reg to rigid approaches (e.g. optical tracking). Surgical plans conformed within the bone cortex by 3-4 mm for the narrowest corridor (superior pubic ramus) and >5 mm for the widest corridor (tear drop). The dKC-Reg algorithm localized the K-wire tip within 1.1 mm and 1.4 degrees and was consistently more accurate than rigid-body tracking (errors up to 9 mm). The system was shown to automatically compute reliable screw trajectories and accurately localize deformed surgical devices (K-wires). Such capability could improve guidance and QA in orthopaedic surgery, where workflow is impeded by manual planning, conventional tool trackers add complexity and cost, rigid tool assumptions are often inaccurate, and qualitative interpretation of complex anatomy from 2D projections is prone to trial-and-error with extended fluoroscopy time.

DeepCADe: A Deep Learning Architecture for the Detection of Lung Nodules in CT Scans

  • Golan, Rotem
2018 Thesis, cited 0 times
Website
Early detection of lung nodules in thoracic Computed Tomography (CT) scans is of great importance for the successful diagnosis and treatment of lung cancer. Due to improvements in screening technologies, and an increased demand for their use, radiologists are required to analyze an ever increasing amount of image data, which can affect the quality of their diagnoses. Computer-Aided Detection (CADe) systems are designed to assist radiologists in this endeavor. In this thesis, we present DeepCADe, a novel CADe system for the detection of lung nodules in thoracic CT scans which produces improved results compared to the state-of-the-art in this field of research. CT scans are grayscale images, so the terms scans and images are used interchangeably in this work. DeepCADe was trained with the publicly available Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) database, which contains 1018 thoracic CT scans with nodules of different shape and size, and is built on a Deep Convolutional Neural Network (DCNN), which is trained using the backpropagation algorithm to extract volumetric features from the input data and detect lung nodules in sub-volumes of CT images. Considering only lung nodules that have been annotated by at least three radiologists, DeepCADe achieves a 2.1% improvement in sensitivity (true positive rate) over the best result in the current published scientific literature, assuming an equal number of false positives (FPs) per scan. More specifically, it achieves a sensitivity of 89.6% with 4 FPs per scan, or a sensitivity of 92.8% with 10 FPs per scan. Furthermore, DeepCADe is validated on a larger number of lung nodules compared to other studies (Table 5.2). This increases the variation in the appearance of nodules and therefore makes their detection by a CADe system more challenging. We study the application of Deep Convolutional Neural Networks (DCNNs) for the detection of lung nodules in thoracic CT scans. We explore some of the meta parameters that affect the performance of such models, which include: 1. the network architecture, i.e. its structure in terms of convolution layers, fully-connected layers, pooling layers, and activation functions, 2. the receptive field of the network, which defines the dimensions of its input, i.e. how much of the CT scan is processed by the network in a single forward pass, 3. a threshold value, which affects the sliding window algorithm with which the network is used to detect nodules in complete CT scans, and 4. the agreement level, which is used to interpret the independent nodule annotations of four experienced radiologists. Finally, we visualize the shape and location of annotated lung nodules and compare them to the output of DeepCADe. This demonstrates the compactness and flexibility in shape of the nodule predictions made by our proposed CADe system. In addition to the 5-fold cross validation results presented in this thesis, these visual results support the applicability of our proposed CADe system in real-world medical practice.

Lung nodule detection in CT images using deep convolutional neural networks

  • Golan, Rotem
  • Jacob, Christian
  • Denzinger, Jörg
2016 Conference Proceedings, cited 26 times
Website
Early detection of lung nodules in thoracic Computed Tomography (CT) scans is of great importance for the successful diagnosis and treatment of lung cancer. Due to improvements in screening technologies, and an increased demand for their use, radiologists are required to analyze an ever increasing amount of image data, which can affect the quality of their diagnoses. Computer-Aided Detection (CADe) systems are designed to assist radiologists in this endeavor. Here, we present a CADe system for the detection of lung nodules in thoracic CT images. Our system is based on (1) the publicly available Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI) database, which contains 1018 thoracic CT scans with nodules of different shape and size, and (2) a deep Convolutional Neural Network (CNN), which is trained, using the back-propagation algorithm, to extract valuable volumetric features from the input data and detect lung nodules in sub-volumes of CT images. Considering only those test nodules that have been annotated by four radiologists, our CADe system achieves a sensitivity (true positive rate) of 78.9% with 20 false positives (FPs) per scan, or a sensitivity of 71.2% with 10 FPs per scan. This is achieved without using any segmentation or additional FP reduction procedures, both of which are commonly used in other CADe systems. Furthermore, our CADe system is validated on a larger number of lung nodules compared to other studies, which increases the variation in their appearance, and therefore, makes their detection by a CADe system more challenging.

Automatic detection of pulmonary nodules in CT images by incorporating 3D tensor filtering with local image feature analysis

  • Gong, J.
  • Liu, J. Y.
  • Wang, L. J.
  • Sun, X. W.
  • Zheng, B.
  • Nie, S. D.
Physica Medica 2018 Journal Article, cited 4 times
Website

Local Binary Pattern-Based Texture Analysis to Predict IDH Genotypes of Glioma Cancer Using Supervised Machine Learning Classifiers

  • Gore, Sonal
  • Jagtap, Jayant
2020 Conference Proceedings, cited 0 times
Website
Nowadays, machine learning-based quantified assessment of glioma has recently gained more attention by researchers in the field of medical image analysis. Such analysis makes use of either hand-crafted radiographic features with radiomic-based methods or auto-extracted features using deep learning-based methods. Radiomic-based methods cover a wide spectrum of radiographic features including texture, shape, volume, intensity, histogram, etc. The objective of the paper is to demonstrate the discriminative role of textures for molecular categorization of glioma using supervised machine learning techniques. This work aims to make state-of-the-art machine learning solutions available for magnetic resonance imaging (MRI)-based genomic analysis of glioma as a simple and sufficient technique based on single feature type, i.e., textures. The potential of this work demonstrates importance of texture features using simple, computationally efficient local binary pattern (LBP) method for isocitrate dehydrogenase (IDH)-based discrimination of glioma as IDH mutant and IDH wild type. Further, such texture-based discriminative analysis alone can definitely facilitate an immediate recommendation for further diagnostic decisions and personalized treatment plans for glioma patients.

IDH-Based Radiogenomic Characterization of Glioma Using Local Ternary Pattern Descriptor Integrated with Radiographic Features and Random Forest Classifier

  • Gore, Sonal
  • Jagtap, Jayant
International Journal of Image and Graphics 2021 Journal Article, cited 0 times
Website
Mutations in family of Isocitrate Dehydrogenase (IDH) gene occur early in oncogenesis, especially with glioma brain tumor. Molecular diagnostic of glioma using machine learning has grabbed attention to some extent from last couple of years. The development of molecular-level predictive approach carries great potential in radiogenomic field. But more focused efforts need to be put to develop such approaches. This study aims to develop an integrative genomic diagnostic method to assess the significant utility of textures combined with other radiographic and clinical features for IDH classification of glioma into IDH mutant and IDH wild type. Random forest classifier is used for classification of combined set of clinical features and radiographic features extracted from axial T2-weighted Magnetic Resonance Imaging (MRI) images of low- and high-grade glioma. Such radiogenomic analysis is performed on The Cancer Genome Atlas (TCGA) data of 74 patients of IDH mutant and 104 patients of IDH wild type. Texture features are extracted using uniform, rotation invariant Local Ternary Pattern (LTP) method. Other features such as shape, first-order statistics, image contrast-based, clinical data like age, histologic grade are combined with LTP features for IDH discrimination. Proposed random forest-assisted model achieved an accuracy of 85.89% with multivariate analysis of integrated set of feature descriptors using Glioblastoma and Low-Grade Glioma dataset available with The Cancer Imaging Archive (TCIA). Such an integrated feature analysis using LTP textures and other descriptors can effectively predict molecular class of glioma as IDH mutant and wild type.

MRI based genomic analysis of glioma using three pathway deep convolutional neural network for IDH classification

  • GORE, SONAL
  • JAGTAP, JAYANT
Turkish Journal of Electrical Engineering & Computer Sciences 2021 Journal Article, cited 0 times
Website

Optimal Statistical incorporation of independent feature Stability information into Radiomics Studies

  • Götz, Michael
  • Maier-Hein, Klaus H
Sci RepScientific reports 2020 Journal Article, cited 0 times
Website
Conducting side experiments termed robustness experiments, to identify features that are stable with respect to rescans, annotation, or other confounding effects is an important element in radiomics research. However, the matter of how to include the finding of these experiments into the model building process still needs to be explored. Three different methods for incorporating prior knowledge into a radiomics modelling process were evaluated: the naive approach (ignoring feature quality), the most common approach consisting of removing unstable features, and a novel approach using data augmentation for information transfer (DAFIT). Multiple experiments were conducted using both synthetic and publicly available real lung imaging patient data. Ignoring additional information from side experiments resulted in significantly overestimated model performances meaning the estimated mean area under the curve achieved with a model was increased. Removing unstable features improved the performance estimation, while slightly decreasing the model performance, i.e. decreasing the area under curve achieved with the model. The proposed approach was superior both in terms of the estimation of the model performance and the actual model performance. Our experiments show that data augmentation can prevent biases in performance estimation and has several advantages over the plain omission of the unstable feature. The actual gain that can be obtained depends on the quality and applicability of the prior information on the features in the given domain. This will be an important topic of future research.

Spatial Decomposition For Robust Domain Adaptation In Prostate Cancer Detection

  • Grebenisan, Andrew
  • Sedghi, Alireza
  • Izard, Jason
  • Siemens, Robert
  • Menard, Alexandre
  • Mousavi, Parvin
2021 Conference Paper, cited 0 times
Website
The utility of high-quality imaging of Prostate Cancer (PCa) using 3.0 Tesla MRI (versus 1.5 Tesla) is well established, yet a vast majority of MRI units across many countries are 1.5 Tesla. Recently, Deep Learning has been applied successfully to augment radiological interpretation of medical images. However, training such models requires very large amount of data, and often the models do not generalize well to data with different acquisition parameters. To address this, we introduce domain standardization, a novel method that enables image synthesis between domains by separating anatomy- and modality-related factors of images. Our results show an improved PCa classification with an AUC of 0.75 compared to traditional transfer learning methods. We envision domain standardization to be applied as a promising tool towards enhancing the interpretation of lower resolution MRI images, reducing the barriers of the potential uptake of deep models for jurisdictions with smaller populations.

Relationship between visceral adipose tissue and genetic mutations (VHL and KDM5C) in clear cell renal cell carcinoma

  • Greco, Federico
  • Mallio, Carlo Augusto
La radiologia medica 2021 Journal Article, cited 0 times
Website

Guest Editorial Deep Learning in Medical Imaging: Overview and Future Promise of an Exciting New Technique

  • Greenspan, Hayit
  • van Ginneken, Bram
  • Summers, Ronald M
IEEE Transactions on Medical Imaging 2016 Journal Article, cited 395 times
Website

Imaging and clinical data archive for head and neck squamous cell carcinoma patients treated with radiotherapy

  • Grossberg, Aaron J
  • Mohamed, Abdallah SR
  • El Halawani, Hesham
  • Bennett, William C
  • Smith, Kirk E
  • Nolan, Tracy S
  • Williams, Bowman
  • Chamchod, Sasikarn
  • Heukelom, Jolien
  • Kantor, Michael E
Scientific data 2018 Journal Article, cited 0 times
Website

Imaging-genomics reveals driving pathways of MRI derived volumetric tumor phenotype features in Glioblastoma

  • Grossmann, Patrick
  • Gutman, David A
  • Dunn, William D
  • Holder, Chad A
  • Aerts, Hugo JWL
BMC Cancer 2016 Journal Article, cited 21 times
Website

Defining the biological and clinical basis of radiomics: towards clinical imaging biomarkers

  • Großmann, P. B. H. J.
  • Grossmann, Patrick Benedict Hans Juan
2018 Thesis, cited 0 times
Website

Machine Learning–based Differentiation of Benign and Premalignant Colorectal Polyps Detected with CT Colonography in an Asymptomatic Screening Population: A Proof-of-Concept Study

  • Sergio Grosu
  • Philipp Wesp
  • Anno Graser
  • Stefan Maurus
  • Christian Schulz
  • Thomas Knösel
  • Clemens C. Cyran
  • Jens Ricke
  • Michael Ingrisch
  • Philipp M. Kazmierczak
RadiologyRadiology 2021 Journal Article, cited 0 times
Website
Background CT colonography does not enable definite differentiation between benign and premalignant colorectal polyps. Purpose To perform machine learning–based differentiation of benign and premalignant colorectal polyps detected with CT colonography in an average-risk asymptomatic colorectal cancer screening sample with external validation using radiomics. Materials and Methods In this secondary analysis of a prospective trial, colorectal polyps of all size categories and morphologies were manually segmented on CT colonographic images and were classified as benign (hyperplastic polyp or regular mucosa) or premalignant (adenoma) according to the histopathologic reference standard. Quantitative image features characterizing shape (n = 14), gray level histogram statistics (n = 18), and image texture (n = 68) were extracted from segmentations after applying 22 image filters, resulting in 1906 feature-filter combinations. Based on these features, a random forest classification algorithm was trained to predict the individual polyp character. Diagnostic performance was validated in an external test set. Results The random forest model was fitted using a training set consisting of 107 colorectal polyps in 63 patients (mean age, 63 years ± 8 [standard deviation]; 40 men) comprising 169 segmentations on CT colonographic images. The external test set included 77 polyps in 59 patients comprising 118 segmentations. Random forest analysis yielded an area under the receiver operating characteristic curve of 0.91 (95% CI: 0.85, 0.96), a sensitivity of 82% (65 of 79) (95% CI: 74%, 91%), and a specificity of 85% (33 of 39) (95% CI: 72%, 95%) in the external test set. In two subgroup analyses of the external test set, the area under the receiver operating characteristic curve was 0.87 in the size category of 6–9 mm and 0.90 in the size category of 10 mm or larger. The most important image feature for decision making (relative importance of 3.7%) was quantifying first-order gray level histogram statistics. Conclusion In this proof-of-concept study, machine learning–based image analysis enabled non