Multi-kernel graph embedding for detection, Gleason grading of prostate cancer via MRI/MRS. Med Image Anal. 2013;17:219-235. [PMID: 23294985 DOI: 10.1016/j.media.2012.10.004]

An Update on MR Spectroscopy in Cancer Management: Advances in Instrumentation, Acquisition, and Analysis

MR spectroscopy (MRS) is a noninvasive imaging method enabling chemical and molecular profiling of tissues in a localized, multiplexed, and nonionizing manner. As metabolic reprogramming is a hallmark of cancer, MRS provides valuable metabolic and molecular information for cancer diagnosis, prognosis, treatment monitoring, and patient management. This review provides an update on the use of MRS for clinical cancer management. The first section includes an overview of the principles of MRS, current methods, and conventional metabolites of interest. The remainder of the review is focused on three key areas: advances in instrumentation, specifically ultrahigh-field-strength MRI scanners and hybrid systems; emerging methods for acquisition, including deuterium imaging, hyperpolarized carbon 13 MRI and MRS, chemical exchange saturation transfer, diffusion-weighted MRS, MR fingerprinting, and fast acquisition; and analysis aided by artificial intelligence. The review concludes with future recommendations to facilitate routine use of MRS in cancer management. Keywords: MR Spectroscopy, Spectroscopic Imaging, Molecular Imaging in Oncology, Metabolic Reprogramming, Clinical Cancer Management © RSNA, 2024.

Semi-Automatic Multiparametric MR Imaging Classification Using Novel Image Input Sequences and 3D Convolutional Neural Networks

The role of multi-parametric magnetic resonance imaging (mp-MRI) is becoming increasingly important in the diagnosis of the clinical severity of prostate cancer (PCa). However, mp-MRI images usually contain several unaligned 3D sequences, such as DWI image sequences and T2-weighted image sequences, and there are many images among the entirety of 3D sequence images that do not contain cancerous tissue, which affects the accuracy of large-scale prostate cancer detection. Therefore, there is a great need for a method that uses accurate computer-aided detection of mp-MRI images and minimizes the influence of useless features. Our proposed PCa detection method is divided into three stages: (i) multimodal image alignment, (ii) automatic cropping of the sequence images to the entire prostate region, and, finally, (iii) combining multiple modal images of each patient into novel 3D sequences and using 3D convolutional neural networks to learn the newly composed 3D sequences with different modal alignments. We arrange the different modal methods to make the model fully learn the cancerous tissue features; then, we predict the clinical severity of PCa and generate a 3D cancer response map for the 3D sequence images from the last convolution layer of the network. The prediction results and 3D response map help to understand the features that the model focuses on during the process of 3D-CNN feature learning. We applied our method to Toho hospital prostate cancer patient data; the AUC (=0.85) results were significantly higher than those of other methods.

Texture analysis on bi-parametric MRI for evaluation of aggressiveness in patients with prostate cancer

PURPOSE

To evaluate the association between texture parameters based on bi-parametric MRI and Gleason score (GS) in patients with prostate cancer (PCa) and to evaluate diagnostic performance of any significant parameter for discriminating clinically significant cancer (CSC, GS ≥ 7) from non-CSC.

METHODS

A total of 116 patients who had been confirmed as prostate adenocarcinoma by radical prostatectomy or biopsy were divided into a training (n = 65) and a validation dataset (n = 51). All of the patients underwent preoperative 3T-MRI. Texture analysis was performed on axial T2WI and ADC maps (generated from b values, 0 and 1000 s/mm²) using dedicated software to cover the whole tumor volume. The correlation coefficient was calculated to evaluate the association between texture parameters and GS, and subsequent multiple regression analyses were applied for the significant parameters. To extract an optimal cut-off value for prediction of CSC, ROC curve analysis was performed.

RESULTS

In the training dataset, gray-level co-occurrence matrix (GLCM) entropy on ADC map was the only significant indicator for GS (coefficient of determination R², 0.4227, P = 0.0034). The AUC of GLCM entropy on ADC map was 0.825 (95% CI 0.711-0.907) with a maximum accuracy of 82%, a sensitivity of 86%, a specificity of 71%. When a cut-off value of 2.92 was applied to the validation dataset, it showed an accuracy of 92%, a sensitivity of 98%, and a specificity of 70%.

CONCLUSION

GLCM entropy on ADC map was associated with GS in patients with PCa and its estimated accuracy for discriminating CSC from non-CSC was 82%.

The role of radiomics in prostate cancer radiotherapy

"Radiomics," as it refers to the extraction and analysis of a large number of advanced quantitative radiological features from medical images using high-throughput methods, is perfectly suited as an engine for effectively sifting through the multiple series of prostate images from before, during, and after radiotherapy (RT). Multiparametric (mp)MRI, planning CT, and cone beam CT (CBCT) routinely acquired throughout RT and the radiomics pipeline are developed for extraction of thousands of variables. Radiomics data are in a format that is appropriate for building descriptive and predictive models relating image features to diagnostic, prognostic, or predictive information. Prediction of Gleason score, the histopathologic cancer grade, has been the mainstay of the radiomic efforts in prostate cancer. While Gleason score (GS) is still the best predictor of treatment outcome, there are other novel applications of quantitative imaging that are tailored to RT. In this review, we summarize the radiomics efforts and discuss several promising concepts such as delta-radiomics and radiogenomics for utilizing image features for assessment of the aggressiveness of prostate cancer and its outcome. We also discuss opportunities for quantitative imaging with the advance of instrumentation in MRI-guided therapies.

Artificial intelligence in multiparametric prostate cancer imaging with focus on deep-learning methods

Prostate cancer represents today the most typical example of a pathology whose diagnosis requires multiparametric imaging, a strategy where multiple imaging techniques are combined to reach an acceptable diagnostic performance. However, the reviewing, weighing and coupling of multiple images not only places additional burden on the radiologist, it also complicates the reviewing process. Prostate cancer imaging has therefore been an important target for the development of computer-aided diagnostic (CAD) tools. In this survey, we discuss the advances in CAD for prostate cancer over the last decades with special attention to the deep-learning techniques that have been designed in the last few years. Moreover, we elaborate and compare the methods employed to deliver the CAD output to the operator for further medical decision making.

Detection of Dominant Intra-prostatic Lesions in Patients With Prostate Cancer Using an Artificial Neural Network and MR Multi-modal Radiomics Analysis

Purpose: The aim of this study was to identify and rank discriminant radiomics features extracted from MR multi-modal images to construct an adaptive model for characterization of Dominant Intra-prostatic Lesions (DILs) from normal prostatic gland tissues (NT).

Methods and Materials: Two cohorts were retrospectively studied: Group A consisted of 98 patients and Group B 19 patients. Two image modalities were acquired using a 3.0T MR scanner: Axial T2 Weighted (T2W) and axial diffusion weighted (DW) imaging. A linear regression method was used to construct apparent diffusion coefficient (ADC) maps from DW images. DILs and the NT in the mirrored location were drawn on each modality. One hundred and sixty-eight radiomics features were extracted from DILs and NT. A Partial-Least-Squares-Correlation (PLSC) with one-way ANOVA along with bootstrapping ratio techniques were recruited to identify and rank the most discriminant latent variables. An artificial neural network (ANN) was constructed based on the optimal latent variable feature to classify the DILs and NTs. Nineteen patients were randomly chosen to test the contour variability effect on the radiomics analysis and the performance of the ANN. Finally, the trained ANN and a two dimension (2D) convolutional sampling method were combined and used to estimate DIL-NT probability map for two test cases.

Results: Among 168 radiomics-based latent variables, only the first four variables of each modality in the PLSC space were found to be significantly different between the DILs and NTs. Area Under Receiver Operating Characteristic (AUROC), Positive Predictive and Negative Predictive values (PPV and NPV) for the conventional method were 94%, 0.95, and 0.92, respectively. When the feature vector was randomly permuted 10,000 times, a very strong permutation-invariant efficiency (p < 0.0001) was achieved. The radiomic-based latent variables of the NTs and DILs showed no statistically significant differences (F_statistic < Fc = 4.11 with Confidence Level of 95% for all 8 variables) against contour variability. Dice coefficients between DIL-NT probability map and physician contours for the two test cases were 0.82 and 0.71, respectively.

Conclusion: This study demonstrates the high performance of combining radiomics information extracted from multimodal MR information such as T2WI and ADC maps, and adaptive models to detect DILs in patients with PCa.

Repeatability of radiomics and machine learning for DWI: Short-term repeatability study of 112 patients with prostate cancer

PURPOSE

To evaluate repeatability of prostate DWI-derived radiomics and machine learning methods for prostate cancer (PCa) characterization.

METHODS

A total of 112 patients with diagnosed PCa underwent 2 prostate MRI examinations (Scan1 and Scan2) performed on the same day. DWI was performed using 12 b-values (0-2000 s/mm² ), post-processed using kurtosis function, and PCa areas were annotated using whole mount prostatectomy sections. A total of 1694 radiomic features including Sobel, Kirch, Gradient, Zernike Moments, Gabor, Haralick, CoLIAGe, Haar wavelet coefficients, 3D analogue to Laws features, 2D contours, and corner detectors were calculated. Radiomics and 4 feature pruning methods (area under the receiver operator characteristic curve, maximum relevance minimum redundancy, Spearman's ρ, Wilcoxon rank-sum) were evaluated in terms of Scan1-Scan2 repeatability using intraclass correlation coefficient (ICC)(3,1). Classification performance for clinically significant and insignificant PCa with Gleason grade groups 1 versus >1 was evaluated by area under the receiver operator characteristic curve in unseen random 30% data split.

RESULTS

The ICC(3,1) values for conventional radiomics and feature pruning methods were in the range of 0.28-0.90. The machine learning classifications varied between Scan1 and Scan2 with % of same class labels between Scan1 and Scan2 in the range of 61-81%. Surface-to-volume ratio and corner detector-based features were among the most represented features with high repeatability, ICC(3,1) >0.75, consistently high ranking using all 4 feature pruning methods, and classification performance with area under the receiver operator characteristic curve >0.70.

CONCLUSION

Surface-to-volume ratio and corner detectors for prostate DWI led to good classification of unseen data and performed similarly in Scan1 and Scan2 in contrast to multiple conventional radiomic features.

Joint Prostate Cancer Detection and Gleason Score Prediction in mp-MRI via FocalNet

Multi-parametric MRI (mp-MRI) is considered the best non-invasive imaging modality for diagnosing prostate cancer (PCa). However, mp-MRI for PCa diagnosis is currently limited by the qualitative or semi-quantitative interpretation criteria, leading to inter-reader variability and a suboptimal ability to assess lesion aggressiveness. Convolutional neural networks (CNNs) are a powerful method to automatically learn the discriminative features for various tasks, including cancer detection. We propose a novel multi-class CNN, FocalNet, to jointly detect PCa lesions and predict their aggressiveness using Gleason score (GS). FocalNet characterizes lesion aggressiveness and fully utilizes distinctive knowledge from mp-MRI. We collected a prostate mp-MRI dataset from 417 patients who underwent 3T mp-MRI exams prior to robotic-assisted laparoscopic prostatectomy. FocalNet was trained and evaluated in this large study cohort with fivefold cross validation. In the free-response receiver operating characteristics (FROC) analysis for lesion detection, FocalNet achieved 89.7% and 87.9% sensitivity for index lesions and clinically significant lesions at one false positive per patient, respectively. For the GS classification, evaluated by the receiver operating characteristics (ROC) analysis, FocalNet received the area under the curve of 0.81 and 0.79 for the classifications of clinically significant PCa (GS ≥ 3 + 4) and PCa with GS ≥ 4 + 3, respectively. With the comparison to the prospective performance of radiologists using the current diagnostic guideline, FocalNet demonstrated comparable detection sensitivity for index lesions and clinically significant lesions, only 3.4% and 1.5% lower than highly experienced radiologists without statistical significance.

A Deep Learning-Based Approach for the Detection and Localization of Prostate Cancer in T2 Magnetic Resonance Images

We address the problem of prostate lesion detection, localization, and segmentation in T2W magnetic resonance (MR) images. We train a deep convolutional encoder-decoder architecture to simultaneously segment the prostate, its anatomical structure, and the malignant lesions. To incorporate the 3D contextual spatial information provided by the MRI series, we propose a novel 3D sliding window approach, which preserves the 2D domain complexity while exploiting 3D information. Experiments on data from 19 patients provided for the public by the Initiative for Collaborative Computer Vision Benchmarking (I2CVB) show that our approach outperforms traditional pattern recognition and machine learning approaches by a significant margin. Particularly, for the task of cancer detection and localization, the system achieves an average AUC of 0.995, an accuracy of 0.894, and a recall of 0.928. The proposed mono-modal deep learning-based system performs comparably to other multi-modal MR-based systems. It could improve the performance of a radiologist in prostate cancer diagnosis and treatment planning.

Radiomics and machine learning of multisequence multiparametric prostate MRI: Towards improved non-invasive prostate cancer characterization

Purpose

To develop and validate a classifier system for prediction of prostate cancer (PCa) Gleason score (GS) using radiomics and texture features of T₂-weighted imaging (T₂w), diffusion weighted imaging (DWI) acquired using high b values, and T₂-mapping (T₂).

Methods

T₂w, DWI (12 b values, 0–2000 s/mm²), and T₂ data sets of 62 patients with histologically confirmed PCa were acquired at 3T using surface array coils. The DWI data sets were post-processed using monoexponential and kurtosis models, while T₂w was standardized to a common scale. Local statistics and 8 different radiomics/texture descriptors were utilized at different configurations to extract a total of 7105 unique per-tumor features. Regularized logistic regression with implicit feature selection and leave pair out cross validation was used to discriminate tumors with 3+3 vs >3+3 GS.

Results

In total, 100 PCa lesions were analysed, of those 20 and 80 had GS of 3+3 and >3+3, respectively. The best model performance was obtained by selecting the top 1% features of T₂w, ADC_m and K with ROC AUC of 0.88 (95% CI of 0.82–0.95). Features from T₂ mapping provided little added value. The most useful texture features were based on the gray-level co-occurrence matrix, Gabor transform, and Zernike moments.

Conclusion

Texture feature analysis of DWI, post-processed using monoexponential and kurtosis models, and T₂w demonstrated good classification performance for GS of PCa. In multisequence setting, the optimal radiomics based texture extraction methods and parameters differed between different image types.

Multiparametric MRI and radiomics in prostate cancer: a review

Multiparametric MRI (mpMRI) is an imaging modality that combines anatomical MR imaging with one or more functional MRI sequences. It has become a versatile tool for detecting and characterising prostate cancer (PCa). The traditional role of mpMRI was confined to PCa staging, but due to the advanced imaging techniques, its role has expanded to various stages in clinical practises including tumour detection, disease monitor during active surveillance and sequential imaging for patient follow-up. Meanwhile, with the growing speed of data generation and the increasing volume of imaging data, it is highly demanded to apply computerised methods to process mpMRI data and extract useful information. Hence quantitative analysis for imaging data using radiomics has become an emerging paradigm. The application of radiomics approaches in prostate cancer has not only enabled automatic localisation of the disease but also provided a non-invasive solution to assess tumour biology (e.g. aggressiveness and the presence of hypoxia). This article reviews mpMRI and its expanding role in PCa detection, staging and patient management. Following that, an overview of prostate radiomics will be provided, with a special focus on its current applications as well as its future directions.

Objective risk stratification of prostate cancer using machine learning and radiomics applied to multiparametric magnetic resonance images

Multiparametric magnetic resonance imaging (mpMRI) has become increasingly important for the clinical assessment of prostate cancer (PCa), but its interpretation is generally variable due to its relatively subjective nature. Radiomics and classification methods have shown potential for improving the accuracy and objectivity of mpMRI-based PCa assessment. However, these studies are limited to a small number of classification methods, evaluation using the AUC score only, and a non-rigorous assessment of all possible combinations of radiomics and classification methods. This paper presents a systematic and rigorous framework comprised of classification, cross-validation and statistical analyses that was developed to identify the best performing classifier for PCa risk stratification based on mpMRI-derived radiomic features derived from a sizeable cohort. This classifier performed well in an independent validation set, including performing better than PI-RADS v2 in some aspects, indicating the value of objectively interpreting mpMRI images using radiomics and classification methods for PCa risk assessment.

Predicting Gleason Score of Prostate Cancer Patients Using Radiomic Analysis

Purpose: Use of quantitative imaging features and encoding the intra-tumoral heterogeneity from multi-parametric magnetic resonance imaging (mpMRI) for the prediction of Gleason score is gaining attention as a non-invasive biomarker for prostate cancer (PCa). This study tested the hypothesis that radiomic features, extracted from mpMRI, could predict the Gleason score pattern of patients with PCa. Methods: This analysis included T2-weighted (T2-WI) and apparent diffusion coefficient (ADC, computed from diffusion-weighted imaging) scans of 99 PCa patients from The Cancer Imaging Archive (TCIA). A total of 41 radiomic features were calculated from a local tumor sub-volume (i.e., regions of interest) that is determined by a centroid coordinate of PCa volume, grouped based on their Gleason score patterns. Kruskal-Wallis and Spearman's rank correlation tests were used to identify features related to Gleason score groups. Random forest (RF) classifier model was used to predict Gleason score groups and identify the most important signature among the 41 radiomic features. Results: Gleason score groups could be discriminated based on zone size percentage, large zone size emphasis and zone size non-uniformity values (p < 0.05). These features also showed a significant correlation between radiomic features and Gleason score groups with a correlation value of -0.35, 0.32, 0.42 for the large zone size emphasis, zone size non-uniformity and zone size percentage, respectively (corrected p < 0.05). RF classifier model achieved an average of the area under the curves of the receiver operating characteristic (ROC) of 83.40, 72.71, and 77.35% to predict Gleason score groups (G1) = 6; 6 < (G2) < (3 + 4) and (G3) ≥ 4 + 3, respectively. Conclusion: Our results suggest that the radiomic features can be used as a non-invasive biomarker to predict the Gleason score of the PCa patients.

Effect of machine learning methods on predicting NSCLC overall survival time based on Radiomics analysis

Background

To investigate the effect of machine learning methods on predicting the Overall Survival (OS) for non-small cell lung cancer based on radiomics features analysis.

Methods

A total of 339 radiomic features were extracted from the segmented tumor volumes of pretreatment computed tomography (CT) images. These radiomic features quantify the tumor phenotypic characteristics on the medical images using tumor shape and size, the intensity statistics and the textures. The performance of 5 feature selection methods and 8 machine learning methods were investigated for OS prediction. The predicted performance was evaluated with concordance index between predicted and true OS for the non-small cell lung cancer patients. The survival curves were evaluated by the Kaplan-Meier algorithm and compared by the log-rank tests.

Results

The gradient boosting linear models based on Cox’s partial likelihood method using the concordance index feature selection method obtained the best performance (Concordance Index: 0.68, 95% Confidence Interval: 0.62~ 0.74).

Conclusions

The preliminary results demonstrated that certain machine learning and radiomics analysis method could predict OS of non-small cell lung cancer accuracy.

Electronic supplementary material

The online version of this article (10.1186/s13014-018-1140-9) contains supplementary material, which is available to authorized users.

Computer-aided diagnosis prior to conventional interpretation of prostate mpMRI: an international multi-reader study

OBJECTIVES

To evaluate if computer-aided diagnosis (CAD) prior to prostate multi-parametric MRI (mpMRI) can improve sensitivity and agreement between radiologists.

METHODS

Nine radiologists (three each high, intermediate, low experience) from eight institutions participated. A total of 163 patients with 3-T mpMRI from 4/2012 to 6/2015 were included: 110 cancer patients with prostatectomy after mpMRI, 53 patients with no lesions on mpMRI and negative TRUS-guided biopsy. Readers were blinded to all outcomes and detected lesions per PI-RADSv2 on mpMRI. After 5 weeks, readers re-evaluated patients using CAD to detect lesions. Prostatectomy specimens registered to MRI were ground truth with index lesions defined on pathology. Sensitivity, specificity and agreement were calculated per patient, lesion level and zone-peripheral (PZ) and transition (TZ).

RESULTS

Index lesion sensitivity was 78.2% for mpMRI alone and 86.3% for CAD-assisted mpMRI (p = 0.013). Sensitivity was comparable for TZ lesions (78.7% vs 78.1%; p = 0.929); CAD improved PZ lesion sensitivity (84% vs 94%; p = 0.003). Improved sensitivity came from lesions scored PI-RADS < 3 as index lesion sensitivity was comparable at PI-RADS ≥ 3 (77.6% vs 78.1%; p = 0.859). Per patient specificity was 57.1% for CAD and 70.4% for mpMRI (p = 0.003). CAD improved agreement between all readers (56.9% vs 71.8%; p < 0.001).

CONCLUSIONS

CAD-assisted mpMRI improved sensitivity and agreement, but decreased specificity, between radiologists of varying experience.

KEY POINTS

• Computer-aided diagnosis (CAD) assists clinicians in detecting prostate cancer on MRI. • CAD assistance improves agreement between radiologists in detecting prostate cancer lesions. • However, this CAD system induces more false positives, particularly for less-experienced clinicians and in the transition zone. • CAD assists radiologists in detecting cancer missed on MRI, suggesting a path for improved diagnostic confidence.

Identifying the morphologic basis for radiomic features in distinguishing different Gleason grades of prostate cancer on MRI: Preliminary findings

Translation of radiomics into the clinic may require a more comprehensive understanding of the underlying morphologic tissue characteristics they reflect. In the context of prostate cancer (PCa), some studies have correlated gross histological measurements of gland lumen, epithelium, and nuclei with disease appearance on MRI. Quantitative histomorphometry (QH), like radiomics for radiologic images, is the computer based extraction of features for describing tumor morphology on digitized tissue images. In this work, we attempt to establish the histomorphometric basis for radiomic features for prostate cancer by (1) identifying the radiomic features from T2w MRI most discriminating of low vs. intermediate/high Gleason score, (2) identifying QH features correlated with the most discriminating radiomic features previously identified, and (3) evaluating the discriminative ability of QH features found to be correlated with spatially co-localized radiomic features. On a cohort of 36 patients (23 for training, 13 for validation), Gabor texture features were identified as being most predictive of Gleason grade on MRI (AUC of 0.69) and gland lumen shape features were identified as the most predictive QH features (AUC = 0.75). Our results suggest that the PCa grade discriminability of Gabor features is a consequence of variations in gland shape and morphology at the tissue level.

Multimodal Radiomic Features for the Predicting Gleason Score of Prostate Cancer

BACKGROUND

Novel radiomic features are enabling the extraction of biological data from routine sequences of MRI images. This study's purpose was to establish a new model, based on the joint intensity matrix (JIM), to predict the Gleason score (GS) of prostate cancer (PCa) patients.

METHODS

A retrospective dataset comprised of the diagnostic imaging data of 99 PCa patients was used, extracted from The Cancer Imaging Archive's (TCIA) T2-Weighted (T2-WI) and apparent diffusion coefficient (ADC) images. Radiomic features derived from JIM and the grey level co-occurrence matrix (GLCM) were extracted from the reported tumor locations. The Kruskal-Wallis test and Spearman's rank correlation identified features related to the GS. The Random Forest classifier model was implemented to identify the best performing signature of JIM and GLCM radiomic features to predict for GS.

RESULTS

Five JIM-derived features: contrast, homogeneity, difference variance, dissimilarity, and inverse difference were independent predictors of GS (p < 0.05). Combined JIM and GLCM analysis provided the best performing area-under-the-curve, with values of 78.40% for GS ≤ 6, 82.35% for GS = 3 + 4, and 64.76% for GS ≥ 4 + 3.

CONCLUSION

This retrospective study produced a novel predictive model for GS by the incorporation of JIM data from standard diagnostic MRI images.

Magnetic resonance imaging (MRI)-based radiomics for prostate cancer radiotherapy

In radiotherapy (RT) of prostate cancer, dose escalation has been shown to reduce biochemical failure. Dose escalation only to determinate prostate tumor habitats has the potential to improve tumor control with less toxicity than when the entire prostate is dose escalated. Other issues in the treatment of the RT patient include the choice of the RT technique (hypo- or standard fractionation) and the use and length of concurrent/adjuvant androgen deprivation therapy (ADT). Up to 50% of high-risk men demonstrate biochemical failure suggesting that additional strategies for defining and treating patients based on improved risk stratification are required. The use of multiparametric MRI (mpMRI) is rapidly gaining momentum in the management of prostate cancer because of its improved diagnostic potential and its ability to combine functional and anatomical information. Currently, the Prostate Imaging, Reporting and Diagnosis System (PIRADS) is the standard of care for region of interest (ROI) identification and risk classification. However, PIRADS was not designed for 3D tumor volume delineation; there is a large degree of subjectivity and PIRADS does not accurately and reproducibly elucidate inter- and intra-lesional spatial heterogeneity. "Radiomics", as it refers to the extraction and analysis of large number of advanced quantitative radiological features from medical images using high throughput methods, is perfectly suited as an engine to effectively sift through the multiple series of prostate mpMRI sequences and quantify regions of interest. The radiomic efforts can be summarized in two main areas: (I) detection/segmentation of the suspicious lesion; and (II) assessment of the aggressiveness of prostate cancer. As related to RT, the goal of the latter is in particular to identify patients at high risk for metastatic disease; and the aim of the former is to identify and segment cancerous lesions and thus provide targets for radiation boost. The article is structured as follows: first, we describe the radiomic approach; and second, we discuss the radiomic pipeline as tailored for RT of prostate cancer. In this process we summarize the current efforts and progress in integrating mpMRI radiomics into the radiotherapeutic management of prostate cancer with emphasis placed on its role in treatment target definition, treatment plan strategizing, and prognostic assessment. The described concepts, methods and tools are not currently applicable to the radiation oncology practice outside of the research setting. More data are required in the form of clinical trials to assess the robustness of radiomics-based predictive models, and to maximize the efficacy of these models.

Automated Detection of Clinically Significant Prostate Cancer in mp-MRI Images Based on an End-to-End Deep Neural Network

Automated methods for detecting clinically significant (CS) prostate cancer (PCa) in multi-parameter magnetic resonance images (mp-MRI) are of high demand. Existing methods typically employ several separate steps, each of which is optimized individually without considering the error tolerance of other steps. As a result, they could either involve unnecessary computational cost or suffer from errors accumulated over steps. In this paper, we present an automated CS PCa detection system, where all steps are optimized jointly in an end-to-end trainable deep neural network. The proposed neural network consists of concatenated subnets: 1) a novel tissue deformation network (TDN) for automated prostate detection and multimodal registration and 2) a dual-path convolutional neural network (CNN) for CS PCa detection. Three types of loss functions, i.e., classification loss, inconsistency loss, and overlap loss, are employed for optimizing all parameters of the proposed TDN and CNN. In the training phase, the two nets mutually affect each other and effectively guide registration and extraction of representative CS PCa-relevant features to achieve results with sufficient accuracy. The entire network is trained in a weakly supervised manner by providing only image-level annotations (i.e., presence/absence of PCa) without exact priors of lesions' locations. Compared with most existing systems which require supervised labels, e.g., manual delineation of PCa lesions, it is much more convenient for clinical usage. Comprehensive evaluation based on fivefold cross validation using 360 patient data demonstrates that our system achieves a high accuracy for CS PCa detection, i.e., a sensitivity of 0.6374 and 0.8978 at 0.1 and 1 false positives per normal/benign patient.

Development of a measure for evaluating lesion-wise performance of CAD algorithms in the context of mpMRI detection of prostate cancer

PURPOSE

Computer-aided detection/diagnosis (CAD) of prostate cancer (PCa) on multiparametric MRI (mpMRI) is an active area of research. In the literature, the performance of predictive models trained to detect PCa on mpMRI has typically been reported in terms of voxel-wise measures such as sensitivity and specificity and/or area under the receiver operating curve (AUC). However, it is unclear whether models that score higher by these measures are actually superior. Here, we propose a novel method for lesion identification as well as novel measures that assess the quality of the detected lesions.

METHODS

A total of 46 axial MRI slices of interest from 34 patients and the associated histopathologic ground truths were used to develop and to characterize the proposed measures. The proposed lesion-wise score s_ℓ is based on the Jaccard similarity index with modifications that emphasize the overlap and colocalization of predicted lesions with ground truth lesions. Thresholding of s_ℓ allowed for the sensitivity and specificity of lesion detection to be assessed, while the proposed lesion-summary score s_σ is a weighted average of s_ℓ s that provides a single summary statistic of lesion detection performance. The proposed measures were used to compare the lesion detection performance of a predictive model vs that of a radiologist on the same data set. The measures were also used to evaluate the degree to which viewing the cancer prediction improved diagnostic accuracy.

RESULTS

The lesion-wise score qualitatively reflected the goodness of predicted lesions over a wide range of values (s_ℓ = 0.1 to s_ℓ = 0.8) and was found to encompass a larger range of values than the Dice coefficient did over the same range of prediction qualities (0-0.9 vs 0-0.75). The lesion-summary score was shown to vary linearly with voxel-wise sensitivity and quadratically with voxel-wise specificity and correlated well with voxel-wise AUC (ρ = 0.68) and the Dice coefficient (ρ = 0.88). Radiologist performance was found to be significantly improved after viewing the model-generated cancer prediction maps as quantified by both s_σ (P = 0.01) and DSC (P = 0.04), with improvements in both lesion detection sensitivity and specificity.

CONCLUSION

The proposed measures allow for the assessment of lesion detection performance, which is most relevant in a clinical setting and would not be possible to do with voxel-wise measures alone.

Intensity-based volumetric registration of magnetic resonance images and whole-mount sections of the prostate

OBJECTIVE

Magnetic Resonance Imaging (MRI) of the prostate provides useful in vivo diagnostic tissue information such as tumor location and aggressiveness, but ex vivo histopathology remains the ground truth. There are several challenges related to the registration of MRI to histopathology. We present a method for registration of standard clinical T2-weighted MRI (T2W-MRI) and transverse histopathology whole-mount (WM) sections of the prostate.

METHODS

An isotropic volume stack was created from the WM sections using 2D rigid and deformable registration combined with linear interpolation. The prostate was segmented manually from the T2W-MRI volume and registered to the WM section volume using a combination of affine and deformable registration. The method was evaluated on a set of 12 patients who had undergone radical prostatectomy. Registration accuracy was assessed using volume overlap (Dice Coefficient, DC) and landmark distances.

RESULTS

The DC was 0.94 for the whole prostate, 0.63 for the peripheral zone and 0.77 for the remaining gland. The landmark distances were on average 5.4 mm.

CONCLUSION

The volume overlap for the whole prostate and remaining gland, as well as the landmark distances indicate good registration accuracy for the proposed method, and shows that it can be highly useful for registering clinical available MRI and WM sections of the prostate.

Emerging Themes in Image Informatics and Molecular Analysis for Digital Pathology

Pathology is essential for research in disease and development, as well as for clinical decision making. For more than 100 years, pathology practice has involved analyzing images of stained, thin tissue sections by a trained human using an optical microscope. Technological advances are now driving major changes in this paradigm toward digital pathology (DP). The digital transformation of pathology goes beyond recording, archiving, and retrieving images, providing new computational tools to inform better decision making for precision medicine. First, we discuss some emerging innovations in both computational image analytics and imaging instrumentation in DP. Second, we discuss molecular contrast in pathology. Molecular DP has traditionally been an extension of pathology with molecularly specific dyes. Label-free, spectroscopic images are rapidly emerging as another important information source, and we describe the benefits and potential of this evolution. Third, we describe multimodal DP, which is enabled by computational algorithms and combines the best characteristics of structural and molecular pathology. Finally, we provide examples of application areas in telepathology, education, and precision medicine. We conclude by discussing challenges and emerging opportunities in this area.

Discriminative Scale Learning (DiScrn): Applications to Prostate Cancer Detection from MRI and Needle Biopsies

There has been recent substantial interest in extracting sub-visual features from medical images for improved disease characterization compared to what might be achievable via visual inspection alone. Features such as Haralick and Gabor can provide a multi-scale representation of the original image by extracting measurements across differently sized neighborhoods. While these multi-scale features are effective, on large-scale digital pathological images, the process of extracting these features is computationally expensive. Moreover for different problems, different scales and neighborhood sizes may be more or less important and thus a large number of features extracted might end up being redundant. In this paper, we present a Discriminative Scale learning (DiScrn) approach that attempts to automatically identify the distinctive scales at which features are able to best separate cancerous from non-cancerous regions on both radiologic and digital pathology tissue images. To evaluate the efficacy of our approach, our approach was employed to detect presence and extent of prostate cancer on a total of 60 MRI and digitized histopathology images. Compared to a multi-scale feature analysis approach invoking features across all scales, DiScrn achieved 66% computational efficiency while also achieving comparable or even better classifier performance.

Computer-aided diagnosis of prostate cancer with MRI

Multi-parametric magnetic resonance imaging (mp-MRI) has an increasingly important role in the diagnosis of prostate cancer. Due to the large amount of data and variations in mp-MRI, tumor detection can be affected by multiple factors, such as the observer's clinical experience, image quality, and appearance of the lesions. In order to improve the quantitative assessment of the disease and reduce the reporting time, various computer-aided diagnosis (CAD) systems have been designed to help radiologists identify lesions. This manuscript presents an overview of the literature regarding prostate CAD using mp-MRI, while focusing on the studies of the most recent five years. Current prostate CAD technologies and their utilization are discussed in this review.

Automated diagnosis of prostate cancer in multi-parametric MRI based on multimodal convolutional neural networks

Automated methods for prostate cancer (PCa) diagnosis in multi-parametric magnetic resonance imaging (MP-MRIs) are critical for alleviating requirements for interpretation of radiographs while helping to improve diagnostic accuracy (Artan et al 2010 IEEE Trans. Image Process. 19 2444-55, Litjens et al 2014 IEEE Trans. Med. Imaging 33 1083-92, Liu et al 2013 SPIE Medical Imaging (International Society for Optics and Photonics) p 86701G, Moradi et al 2012 J. Magn. Reson. Imaging 35 1403-13, Niaf et al 2014 IEEE Trans. Image Process. 23 979-91, Niaf et al 2012 Phys. Med. Biol. 57 3833, Peng et al 2013a SPIE Medical Imaging (International Society for Optics and Photonics) p 86701H, Peng et al 2013b Radiology 267 787-96, Wang et al 2014 BioMed. Res. Int. 2014). This paper presents an automated method based on multimodal convolutional neural networks (CNNs) for two PCa diagnostic tasks: (1) distinguishing between cancerous and noncancerous tissues and (2) distinguishing between clinically significant (CS) and indolent PCa. Specifically, our multimodal CNNs effectively fuse apparent diffusion coefficients (ADCs) and T2-weighted MP-MRI images (T2WIs). To effectively fuse ADCs and T2WIs we design a new similarity loss function to enforce consistent features being extracted from both ADCs and T2WIs. The similarity loss is combined with the conventional classification loss functions and integrated into the back-propagation procedure of CNN training. The similarity loss enables better fusion results than existing methods as the feature learning processes of both modalities are mutually guided, jointly facilitating CNN to 'see' the true visual patterns of PCa. The classification results of multimodal CNNs are further combined with the results based on handcrafted features using a support vector machine classifier. To achieve a satisfactory accuracy for clinical use, we comprehensively investigate three critical factors which could greatly affect the performance of our multimodal CNNs but have not been carefully studied previously. (1) Given limited training data, how can these be augmented in sufficient numbers and variety for fine-tuning deep CNN networks for PCa diagnosis? (2) How can multimodal MP-MRI information be effectively combined in CNNs? (3) What is the impact of different CNN architectures on the accuracy of PCa diagnosis? Experimental results on extensive clinical data from 364 patients with a total of 463 PCa lesions and 450 identified noncancerous image patches demonstrate that our system can achieve a sensitivity of 89.85% and a specificity of 95.83% for distinguishing cancer from noncancerous tissues and a sensitivity of 100% and a specificity of 76.92% for distinguishing indolent PCa from CS PCa. This result is significantly superior to the state-of-the-art method relying on handcrafted features.

氢质子磁共振波谱对胰腺癌分析及其分化程度相关性研究

目的

探讨氢质子磁共振波谱(¹H magnetic resonance spectroscopy, ¹H MRS)分析胰腺癌瘤体与瘤旁导管上皮内瘤变(pancreatic duct intraepithelial neoplasia, Pan IN)病变及肿瘤不同分化程度的代谢物差异.

方法

病理确诊为胰腺导管腺癌的患者47例(低分化17例、中分化30例), 术前均行¹H MRS检查, 使用呼吸门控的抑水点分辨波谱序列对肿瘤的瘤体、瘤旁组织进行¹H MRS检测. 分析出每个¹H MRS数据的胆碱峰(choline-containing metabolites, CCM)/脂肪峰(lipid, Lip)、胆固醇及不饱和脂肪酸峰(cholesterol and unsaturated fatty acids, Chol+Unsat)/Lip、Chol+Unsat/CCM的峰下面积比, 采用配对样本t检验比较瘤体和瘤旁组织的代谢物差异, 用独立样本t检验比较胰腺导管腺癌低分化组和中分化组的代谢物差异.

结果

同时获得瘤体和瘤旁数据共24例, 瘤体组织的CCM/Lip高于瘤旁组织(0.266±0.084 vs 0.200±0.081), 瘤体组织的Chol+Unsat/Lip高于瘤旁组织(0.324±0.109 vs 0.258±0.092), 差异均有统计学意义(P<0.05), 瘤体和瘤旁组织的Chol+Unsat/CCM无统计学差异; 胰腺低分化和中分化导管腺癌的CCM/Lip、Chol+Unsat/Lip、Chol+Unsat/CCM无统计学差异.

结论

¹H MRS对鉴别胰腺癌与瘤旁Pan IN病变具有一定意义, 但不可预测其肿瘤分化程度.

A ℓ2, 1 norm regularized multi-kernel learning for false positive reduction in Lung nodule CAD

OBJECTIVE

The aim of this paper is to describe a novel algorithm for False Positive Reduction in lung nodule Computer Aided Detection(CAD).

METHODS

In this paper, we describes a new CT lung CAD method which aims to detect solid nodules. Specially, we proposed a multi-kernel classifier with a ℓ_{2, 1} norm regularizer for heterogeneous feature fusion and selection from the feature subset level, and designed two efficient strategies to optimize the parameters of kernel weights in non-smooth ℓ_{2, 1} regularized multiple kernel learning algorithm. The first optimization algorithm adapts a proximal gradient method for solving the ℓ_{2, 1} norm of kernel weights, and use an accelerated method based on FISTA; the second one employs an iterative scheme based on an approximate gradient descent method.

RESULTS

The results demonstrates that the FISTA-style accelerated proximal descent method is efficient for the ℓ_{2, 1} norm formulation of multiple kernel learning with the theoretical guarantee of the convergence rate. Moreover, the experimental results demonstrate the effectiveness of the proposed methods in terms of Geometric mean (G-mean) and Area under the ROC curve (AUC), and significantly outperforms the competing methods.

CONCLUSIONS

The proposed approach exhibits some remarkable advantages both in heterogeneous feature subsets fusion and classification phases. Compared with the fusion strategies of feature-level and decision level, the proposed ℓ_{2, 1} norm multi-kernel learning algorithm is able to accurately fuse the complementary and heterogeneous feature sets, and automatically prune the irrelevant and redundant feature subsets to form a more discriminative feature set, leading a promising classification performance. Moreover, the proposed algorithm consistently outperforms the comparable classification approaches in the literature.

Dimensionality reduction-based fusion approaches for imaging and non-imaging biomedical data: concepts, workflow, and use-cases

BACKGROUND

With a wide array of multi-modal, multi-protocol, and multi-scale biomedical data being routinely acquired for disease characterization, there is a pressing need for quantitative tools to combine these varied channels of information. The goal of these integrated predictors is to combine these varied sources of information, while improving on the predictive ability of any individual modality. A number of application-specific data fusion methods have been previously proposed in the literature which have attempted to reconcile the differences in dimensionalities and length scales across different modalities. Our objective in this paper was to help identify metholodological choices that need to be made in order to build a data fusion technique, as it is not always clear which strategy is optimal for a particular problem. As a comprehensive review of all possible data fusion methods was outside the scope of this paper, we have focused on fusion approaches that employ dimensionality reduction (DR).

METHODS

In this work, we quantitatively evaluate 4 non-overlapping existing instantiations of DR-based data fusion, within 3 different biomedical applications comprising over 100 studies. These instantiations utilized different knowledge representation and knowledge fusion methods, allowing us to examine the interplay of these modules in the context of data fusion. The use cases considered in this work involve the integration of (a) radiomics features from T2w MRI with peak area features from MR spectroscopy for identification of prostate cancer in vivo, (b) histomorphometric features (quantitative features extracted from histopathology) with protein mass spectrometry features for predicting 5 year biochemical recurrence in prostate cancer patients, and (c) volumetric measurements on T1w MRI with protein expression features to discriminate between patients with and without Alzheimers' Disease.

RESULTS AND CONCLUSIONS

Our preliminary results in these specific use cases indicated that the use of kernel representations in conjunction with DR-based fusion may be most effective, as a weighted multi-kernel-based DR approach resulted in the highest area under the ROC curve of over 0.8. By contrast non-optimized DR-based representation and fusion methods yielded the worst predictive performance across all 3 applications. Our results suggest that when the individual modalities demonstrate relatively poor discriminability, many of the data fusion methods may not yield accurate, discriminatory representations either. In summary, to outperform the predictive ability of individual modalities, methodological choices for data fusion must explicitly account for the sparsity of and noise in the feature space.

Computer aided diagnosis of prostate cancer: A texton based approach

PURPOSE

In this paper the authors propose a texton based prostate computer aided diagnosis approach which bypasses the typical feature extraction process such as filtering and convolution which can be computationally expensive. The study focuses the peripheral zone because 75% of prostate cancers start within this region and the majority of prostate cancers arising within this region are more aggressive than those arising in the transitional zone.

METHODS

For the model development, square patches were extracted at random locations from malignant and benign regions. Subsequently, extracted patches were aggregated and clustered using k-means clustering to generate textons that represent both regions. All textons together form a texton dictionary, which was used to construct a texton map for every peripheral zone in the training images. Based on the texton map, histogram models for each malignant and benign tissue samples were constructed and used as a feature vector to train our classifiers. In the testing phase, four machine learning algorithms were employed to classify each unknown sample tissue based on its corresponding feature vector.

RESULTS

The proposed method was tested on 418 T2-W MR images taken from 45 patients. Evaluation results show that the best three classifiers were Bayesian network (Az = 92.8% ± 5.9%), random forest (89.5% ± 7.1%), and k-NN (86.9% ± 7.5%). These results are comparable to the state-of-the-art in the literature.

CONCLUSIONS

The authors have developed a prostate computer aided diagnosis method based on textons using a single modality of T2-W MRI without the need for the typical feature extraction methods, such as filtering and convolution. The proposed method could form a solid basis for a multimodality magnetic resonance imaging based systems.

In vivo MRI based prostate cancer localization with random forests and auto-context model

Prostate cancer is one of the major causes of cancer death for men. Magnetic resonance (MR) imaging is being increasingly used as an important modality to localize prostate cancer. Therefore, localizing prostate cancer in MRI with automated detection methods has become an active area of research. Many methods have been proposed for this task. However, most of previous methods focused on identifying cancer only in the peripheral zone (PZ), or classifying suspicious cancer ROIs into benign tissue and cancer tissue. Few works have been done on developing a fully automatic method for cancer localization in the entire prostate region, including central gland (CG) and transition zone (TZ). In this paper, we propose a novel learning-based multi-source integration framework to directly localize prostate cancer regions from in vivo MRI. We employ random forests to effectively integrate features from multi-source images together for cancer localization. Here, multi-source images include initially the multi-parametric MRIs (i.e., T2, DWI, and dADC) and later also the iteratively-estimated and refined tissue probability map of prostate cancer. Experimental results on 26 real patient data show that our method can accurately localize cancerous sections. The higher section-based evaluation (SBE), combined with the ROC analysis result of individual patients, shows that the proposed method is promising for in vivo MRI based prostate cancer localization, which can be used for guiding prostate biopsy, targeting the tumor in focal therapy planning, triage and follow-up of patients with active surveillance, as well as the decision making in treatment selection. The common ROC analysis with the AUC value of 0.832 and also the ROI-based ROC analysis with the AUC value of 0.883 both illustrate the effectiveness of our proposed method.

Prostate cancer radiomics and the promise of radiogenomics

Prostate cancer exhibits intra-tumoral heterogeneity that we hypothesize to be the leading confounding factor contributing to the underperformance of the current pre-treatment clinical-pathological and genomic assessment. These limitations impose an urgent need to develop better computational tools to identify men with low risk of prostate cancer versus others that may be at risk for developing metastatic cancer. The patient stratification will directly translate to patient treatments, wherein decisions regarding active surveillance or intensified therapy are made. Multiparametric MRI (mpMRI) provides the platform to investigate tumor heterogeneity by mapping the individual tumor habitats. We hypothesize that quantitative assessment (radiomics) of these habitats results in distinct combinations of descriptors that reveal regions with different physiologies and phenotypes. Radiogenomics, a discipline connecting tumor morphology described by radiomic and its genome described by the genomic data, has the potential to derive "radio phenotypes" that both correlate to and complement existing validated genomic risk stratification biomarkers. In this article we first describe the radiomic pipeline, tailored for analysis of prostate mpMRI, and in the process we introduce our particular implementations of radiomics modules. We also summarize the efforts in the radiomics field related to prostate cancer diagnosis and assessment of aggressiveness. Finally, we describe our results from radiogenomic analysis, based on mpMRI-Ultrasound (MRI-US) biopsies and discuss the potential of future applications of this technique. The mpMRI radiomics data indicate that the platform would significantly improve the biopsy targeting of prostate habitats through better recognition of indolent versus aggressive disease, thereby facilitating a more personalized approach to prostate cancer management. The expectation to non-invasively identify habitats with high probability of housing aggressive cancers would result in directed biopsies that are more informative and actionable. Conversely, providing evidence for lack of disease would reduce the incidence of non-informative biopsies. In radiotherapy of prostate cancer, dose escalation has been shown to reduce biochemical failure. Dose escalation only to determinate prostate habitats has the potential to improve tumor control with less toxicity than when the entire prostate is dose escalated.

Computer-aided Detection of Prostate Cancer with MRI: Technology and Applications

One in six men will develop prostate cancer in his lifetime. Early detection and accurate diagnosis of the disease can improve cancer survival and reduce treatment costs. Recently, imaging of prostate cancer has greatly advanced since the introduction of multiparametric magnetic resonance imaging (mp-MRI). Mp-MRI consists of T2-weighted sequences combined with functional sequences including dynamic contrast-enhanced MRI, diffusion-weighted MRI, and magnetic resonance spectroscopy imaging. Because of the big data and variations in imaging sequences, detection can be affected by multiple factors such as observer variability and visibility and complexity of the lesions. To improve quantitative assessment of the disease, various computer-aided detection systems have been designed to help radiologists in their clinical practice. This review paper presents an overview of literatures on computer-aided detection of prostate cancer with mp-MRI, which include the technology and its applications. The aim of the survey is threefold: an introduction for those new to the field, an overview for those working in the field, and a reference for those searching for literature on a specific application.

Evaluation of an Automated Analysis Tool for Prostate Cancer Prediction Using Multiparametric Magnetic Resonance Imaging

OBJECTIVE

To evaluate the diagnostic performance of an automated analysis tool for the assessment of prostate cancer based on multiparametric magnetic resonance imaging (mpMRI) of the prostate.

METHODS

A fully automated analysis tool was used for a retrospective analysis of mpMRI sets (T2-weighted, T1-weighted dynamic contrast-enhanced, and diffusion-weighted sequences). The software provided a malignancy prediction value for each image pixel, defined as Malignancy Attention Index (MAI) that can be depicted as a colour map overlay on the original images. The malignancy maps were compared to histopathology derived from a combination of MRI-targeted and systematic transperineal MRI/TRUS-fusion biopsies.

RESULTS

In total, mpMRI data of 45 patients were evaluated. With a sensitivity of 85.7% (with 95% CI of 65.4-95.0), a specificity of 87.5% (with 95% CI of 69.0-95.7) and a diagnostic accuracy of 86.7% (with 95% CI of 73.8-93.8) for detection of prostate cancer, the automated analysis results corresponded well with the reported diagnostic accuracies by human readers based on the PI-RADS system in the current literature.

CONCLUSION

The study revealed comparable diagnostic accuracies for the detection of prostate cancer of a user-independent MAI-based automated analysis tool and PI-RADS-scoring-based human reader analysis of mpMRI. Thus, the analysis tool could serve as a detection support system for less experienced readers. The results of the study also suggest the potential of MAI-based analysis for advanced lesion assessments, such as cancer extent and staging prediction.

Framework for 3D histologic reconstruction and fusion with in vivo MRI: Preliminary results of characterizing pulmonary inflammation in a mouse model

PURPOSE

Pulmonary inflammation is associated with a variety of diseases. Assessing pulmonary inflammation on in vivo imaging may facilitate the early detection and treatment of lung diseases. Although routinely used in thoracic imaging, computed tomography has thus far not been compellingly shown to characterize inflammation in vivo. Alternatively, magnetic resonance imaging (MRI) is a nonionizing radiation technique to better visualize and characterize pulmonary tissue. Prior to routine adoption of MRI for early characterization of inflammation in humans, a rigorous and quantitative characterization of the utility of MRI to identify inflammation is required. Such characterization may be achieved by considering ex vivo histology as the ground truth, since it enables the definitive spatial assessment of inflammation. In this study, the authors introduce a novel framework to integrate 2D histology, ex vivo and in vivo imaging to enable the mapping of the extent of disease from ex vivo histology onto in vivo imaging, with the goal of facilitating computerized feature analysis and interrogation of disease appearance on in vivo imaging. The authors' framework was evaluated in a preclinical preliminary study aimed to identify computer extracted features on in vivo MRI associated with chronic pulmonary inflammation.

METHODS

The authors' image analytics framework first involves reconstructing the histologic volume in 3D from individual histology slices. Second, the authors map the disease ground truth onto in vivo MRI via coregistration with 3D histology using the ex vivo lung MRI as a conduit. Finally, computerized feature analysis of the disease extent is performed to identify candidate in vivo imaging signatures of disease presence and extent.

RESULTS

The authors evaluated the framework by assessing the quality of the 3D histology reconstruction and the histology-MRI fusion, in the context of an initial use case involving characterization of chronic inflammation in a mouse model. The authors' evaluation considered three mice, two with an inflammation phenotype and one control. The authors' iterative 3D histology reconstruction yielded a 70.1% ± 2.7% overlap with the ex vivo MRI volume. Across a total of 17 anatomic landmarks manually delineated at the division of airways, the target registration error between the ex vivo MRI and 3D histology reconstruction was 0.85 ± 0.44 mm, suggesting that a good alignment of the ex vivo 3D histology and ex vivo MRI had been achieved. The 3D histology-in vivo MRI coregistered volumes resulted in an overlap of 73.7% ± 0.9%. Preliminary computerized feature analysis was performed on an additional four control mice, for a total of seven mice considered in this study. Gabor texture filters appeared to best capture differences between the inflamed and noninflamed regions on MRI.

CONCLUSIONS

The authors' 3D histology reconstruction and multimodal registration framework were successfully employed to reconstruct the histology volume of the lung and fuse it with in vivo MRI to create a ground truth map for inflammation on in vivo MRI. The analytic platform presented here lays the framework for a rigorous validation of the identified imaging features for chronic lung inflammation on MRI in a large prospective cohort.

Exploratory Study to Identify Radiomics Classifiers for Lung Cancer Histology

Background

Radiomics can quantify tumor phenotypic characteristics non-invasively by applying feature algorithms to medical imaging data. In this study of lung cancer patients, we investigated the association between radiomic features and the tumor histologic subtypes (adenocarcinoma and squamous cell carcinoma). Furthermore, in order to predict histologic subtypes, we employed machine-learning methods and independently evaluated their prediction performance.

Methods

Two independent radiomic cohorts with a combined size of 350 patients were included in our analysis. A total of 440 radiomic features were extracted from the segmented tumor volumes of pretreatment CT images. These radiomic features quantify tumor phenotypic characteristics on medical images using tumor shape and size, intensity statistics, and texture. Univariate analysis was performed to assess each feature’s association with the histological subtypes. In our multivariate analysis, we investigated 24 feature selection methods and 3 classification methods for histology prediction. Multivariate models were trained on the training cohort and their performance was evaluated on the independent validation cohort using the area under ROC curve (AUC). Histology was determined from surgical specimen.

Results

In our univariate analysis, we observed that fifty-three radiomic features were significantly associated with tumor histology. In multivariate analysis, feature selection methods ReliefF and its variants showed higher prediction accuracy as compared to other methods. We found that Naive Baye’s classifier outperforms other classifiers and achieved the highest AUC (0.72; p-value = 2.3 × 10⁻⁷) with five features: Stats_min, Wavelet_HLL_rlgl_lowGrayLevelRunEmphasis, Wavelet_HHL_stats_median, Wavelet_HLL_stats_skewness, and Wavelet_HLH_glcm_clusShade.

Conclusion

Histological subtypes can influence the choice of a treatment/therapy for lung cancer patients. We observed that radiomic features show significant association with the lung tumor histology. Moreover, radiomics-based multivariate classifiers were independently validated for the prediction of histological subtypes. Despite achieving lower than optimal prediction accuracy (AUC 0.72), our analysis highlights the impressive potential of non-invasive and cost-effective radiomics for precision medicine. Further research in this direction could lead us to optimal performance and therefore to clinical applicability, which could enhance the efficiency and efficacy of cancer care.

Automated prostate cancer detection using T2-weighted and high-b-value diffusion-weighted magnetic resonance imaging

PURPOSE

The authors propose a computer-aided diagnosis (CAD) system for prostate cancer to aid in improving the accuracy, reproducibility, and standardization of multiparametric magnetic resonance imaging (MRI).

METHODS

The proposed system utilizes two MRI sequences [T2-weighted MRI and high-b-value (b = 2000 s/mm(2)) diffusion-weighted imaging (DWI)] and texture features based on local binary patterns. A three-stage feature selection method is employed to provide the most discriminative features. The authors included a total of 244 patients. Training the CAD system on 108 patients (78 MR-positive prostate cancers and 105 benign MR-positive lesions), two validation studies were retrospectively performed on 136 patients (68 MR-positive prostate cancers, 111 benign MR-positive lesions, and 117 MR-negative benign lesions).

RESULTS

In distinguishing cancer from MR-positive benign lesions, an area under receiver operating characteristic curve (AUC) of 0.83 [95% confidence interval (CI): 0.76-0.89] was achieved. For cancer vs MR-positive or MR-negative benign lesions, the authors obtained an AUC of 0.89 AUC (95% CI: 0.84-0.93). The performance of the CAD system was not dependent on the specific regions of the prostate, e.g., a peripheral zone or transition zone. Moreover, the CAD system outperformed other combinations of MRI sequences: T2W MRI, high-b-value DWI, and the standard apparent diffusion coefficient (ADC) map of DWI.

CONCLUSIONS

The novel CAD system is able to detect the discriminative texture features for cancer detection and localization and is a promising tool for improving the quality and efficiency of prostate cancer diagnosis.

Patch-Based Label Fusion for Automatic Multi-Atlas-Based Prostate Segmentation in MR Images

In this paper, we propose a 3D multi-atlas-based prostate segmentation method for MR images, which utilizes patch-based label fusion strategy. The atlases with the most similar appearance are selected to serve as the best subjects in the label fusion. A local patch-based atlas fusion is performed using voxel weighting based on anatomical signature. This segmentation technique was validated with a clinical study of 13 patients and its accuracy was assessed using the physicians' manual segmentations (gold standard). Dice volumetric overlapping was used to quantify the difference between the automatic and manual segmentation. In summary, we have developed a new prostate MR segmentation approach based on nonlocal patch-based label fusion, demonstrated its clinical feasibility, and validated its accuracy with manual segmentations.

Clinical application of magnetic resonance spectroscopy in diagnosis of pancreatic cancer

Pancreatic cancer (PC) is one of the most frequent malignant tumors of the digestive system, which is difficultly detected and highly aggressive. More than 80% of patients with PC present with advanced disease that is incurable by surgery. Thus, early diagnosis and surgery before frank invasion occurs are critical for improving PC patients' outcomes. Magnetic resonance spectroscopy (MRS) is conducive to screening, early diagnosis and differential diagnosis of PC. Nowadays, MRS is preeminently a tool for nondestructive chemical analysis and metabolic profiling. MRS is expected to be a sensitive and accurate method for PC diagnosis and differential diagnosis, for tracking tumor change and for assessing treatment response.

Computer-extracted Features Can Distinguish Noncancerous Confounding Disease from Prostatic Adenocarcinoma at Multiparametric MR Imaging

PURPOSE

To determine the best features to discriminate prostate cancer from benign disease and its relationship to benign disease class and cancer grade.

MATERIALS AND METHODS

The institutional review board approved this study and waived the need for informed consent. A retrospective cohort of 70 patients (age range, 48-70 years; median, 62 years), all of whom were scheduled to undergo radical prostatectomy and underwent preoperative 3-T multiparametric magnetic resonance (MR) imaging, including T2-weighted, diffusion-weighted, and dynamic contrast material-enhanced imaging, were included. The digitized prostatectomy slides were annotated for cancer and noncancerous disease and coregistered to MR imaging with an interactive deformable coregistration scheme. Computer-identified features for each of the noncancerous disease categories (eg, benign prostatic hyperplasia [BPH], prostatic intraepithelial neoplasia [PIN], inflammation, and atrophy) and prostate cancer were extracted. Feature selection was performed to identify the features with the highest discriminatory power. The performance of these five features was evaluated by using the area under the receiver operating characteristic curve (AUC).

RESULTS

High-b-value diffusion-weighted images were more discriminative in distinguishing BPH from prostate cancer than apparent diffusion coefficient, which was most suitable for distinguishing PIN from prostate cancer. The focal appearance of lesions on dynamic contrast-enhanced images may help discriminate atrophy and inflammation from cancer. Which imaging features are discriminative for different benign lesions is influenced by cancer grade. The apparent diffusion coefficient appeared to be the most discriminative feature in identifying high-grade cancer. Classification results showed increased performance by taking into account specific benign types (AUC = 0.70) compared with grouping all noncancerous findings together (AUC = 0.62).

CONCLUSION

The best features with which to discriminate prostate cancer from noncancerous benign disease depend on the type of benign disease and cancer grade. Use of the best features may result in better diagnostic performance.

Automatic classification of prostate cancer Gleason scores from multiparametric magnetic resonance images

Noninvasive, radiological image-based detection and stratification of Gleason patterns can impact clinical outcomes, treatment selection, and the determination of disease status at diagnosis without subjecting patients to surgical biopsies. We present machine learning-based automatic classification of prostate cancer aggressiveness by combining apparent diffusion coefficient (ADC) and T2-weighted (T2-w) MRI-based texture features. Our approach achieved reasonably accurate classification of Gleason scores (GS) 6(3 + 3) vs. ≥7 and 7(3 + 4) vs. 7(4 + 3) despite the presence of highly unbalanced samples by using two different sample augmentation techniques followed by feature selection-based classification. Our method distinguished between GS 6(3 + 3) and ≥7 cancers with 93% accuracy for cancers occurring in both peripheral (PZ) and transition (TZ) zones and 92% for cancers occurring in the PZ alone. Our approach distinguished the GS 7(3 + 4) from GS 7(4 + 3) with 92% accuracy for cancers occurring in both the PZ and TZ and with 93% for cancers occurring in the PZ alone. In comparison, a classifier using only the ADC mean achieved a top accuracy of 58% for distinguishing GS 6(3 + 3) vs. GS ≥7 for cancers occurring in PZ and TZ and 63% for cancers occurring in PZ alone. The same classifier achieved an accuracy of 59% for distinguishing GS 7(3 + 4) from GS 7(4 + 3) occurring in the PZ and TZ and 60% for cancers occurring in PZ alone. Separate analysis of the cancers occurring in TZ alone was not performed owing to the limited number of samples. Our results suggest that texture features derived from ADC and T2-w MRI together with sample augmentation can help to obtain reasonably accurate classification of Gleason patterns.

Automated prostate cancer detection via comprehensive multi-parametric magnetic resonance imaging texture feature models

BACKGROUND

Prostate cancer is the most common form of cancer and the second leading cause of cancer death in North America. Auto-detection of prostate cancer can play a major role in early detection of prostate cancer, which has a significant impact on patient survival rates. While multi-parametric magnetic resonance imaging (MP-MRI) has shown promise in diagnosis of prostate cancer, the existing auto-detection algorithms do not take advantage of abundance of data available in MP-MRI to improve detection accuracy. The goal of this research was to design a radiomics-based auto-detection method for prostate cancer via utilizing MP-MRI data.

METHODS

In this work, we present new MP-MRI texture feature models for radiomics-driven detection of prostate cancer. In addition to commonly used non-invasive imaging sequences in conventional MP-MRI, namely T2-weighted MRI (T2w) and diffusion-weighted imaging (DWI), our proposed MP-MRI texture feature models incorporate computed high-b DWI (CHB-DWI) and a new diffusion imaging modality called correlated diffusion imaging (CDI). Moreover, the proposed texture feature models incorporate features from individual b-value images. A comprehensive set of texture features was calculated for both the conventional MP-MRI and new MP-MRI texture feature models. We performed feature selection analysis for each individual modality and then combined best features from each modality to construct the optimized texture feature models.

RESULTS

The performance of the proposed MP-MRI texture feature models was evaluated via leave-one-patient-out cross-validation using a support vector machine (SVM) classifier trained on 40,975 cancerous and healthy tissue samples obtained from real clinical MP-MRI datasets. The proposed MP-MRI texture feature models outperformed the conventional model (i.e., T2w+DWI) with regard to cancer detection accuracy.

CONCLUSIONS

Comprehensive texture feature models were developed for improved radiomics-driven detection of prostate cancer using MP-MRI. Using a comprehensive set of texture features and a feature selection method, optimal texture feature models were constructed that improved the prostate cancer auto-detection significantly compared to conventional MP-MRI texture feature models.

Interactive Feature Space Explorer© for multi-modal magnetic resonance imaging

Wider information content of multi-modal biomedical imaging is advantageous for detection, diagnosis and prognosis of various pathologies. However, the necessity to evaluate a large number images might hinder these advantages and reduce the efficiency. Herein, a new computer aided approach based on the utilization of feature space (FS) with reduced reliance on multiple image evaluations is proposed for research and routine clinical use. The method introduces the physician experience into the discovery process of FS biomarkers for addressing biological complexity, e.g., disease heterogeneity. This, in turn, elucidates relevant biophysical information which would not be available when automated algorithms are utilized. Accordingly, the prototype platform was designed and built for interactively investigating the features and their corresponding anatomic loci in order to identify pathologic FS regions. While the platform might be potentially beneficial in decision support generally and specifically for evaluating outlier cases, it is also potentially suitable for accurate ground truth determination in FS for algorithm development. Initial assessments conducted on two different pathologies from two different institutions provided valuable biophysical perspective. Investigations of the prostate magnetic resonance imaging data resulted in locating a potential aggressiveness biomarker in prostate cancer. Preliminary findings on renal cell carcinoma imaging data demonstrated potential for characterization of disease subtypes in the FS.