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

Comparison of diagnostic accuracy of radiomics parameter maps and standard reconstruction for the detection of liver lesions in computed tomography

Background

The liver is a frequent location of metastatic disease in various malignant tumor entities. Computed tomography (CT) is the most frequently employed modality for initial diagnosis. However, liver metastases may only be delineated vaguely on CT. Calculating radiomics features in feature maps can unravel textures not visible to the human eye on a standard CT reconstruction (SCTR). This study aimed to investigate the comparative diagnostic accuracy of radiomics feature maps and SCTR for liver metastases.

Materials and methods

Forty-seven patients with hepatic metastatic colorectal cancer were retrospectively enrolled. Whole-liver maps of original radiomics features were generated. A representative feature was selected for each feature class based on the visualization of example lesions from five patients. These maps and the conventional CT image data were viewed and evaluated by four readers in terms of liver parenchyma, number of lesions, visual contrast of lesions and diagnostic confidence. T-tests and chi²-tests were performed with a significance cut off of p<0.05 to compare the feature maps with SCRT, and the data were visualized as boxplots.

Results

Regarding the number of lesions detected, SCTR showed superior performance compared to radiomics maps. However, the feature map for firstorder RootMeanSquared was ranked superior in terms of very high visual contrast in 57.4% of cases, compared to 41.0% in standard reconstructions (p < 0.001). All other radiomics maps ranked significantly lower in visual contrast when compared to SCTR. For diagnostic confidence, firstorder RootMeanSquared reached very high ratings in 47.9% of cases, compared to 62.8% for SCTR (p < 0.001). The conventional CT images showed superior results in all categories for the other features investigated.

Conclusion

The application of firstorder RootMeanSquared feature maps may help visualize faintly demarcated liver lesions by increasing visual contrast. However, reading of SCTR remains necessary for diagnostic confidence.

Deep learning prediction of stroke thrombus red blood cell content from multiparametric MRI

BACKGROUND AND PURPOSE

Thrombus red blood cell (RBC) content has been shown to be a significant factor influencing the efficacy of acute ischemic stroke treatment. In this study, our objective was to evaluate the ability of convolutional neural networks (CNNs) to predict ischemic stroke thrombus RBC content using multiparametric MR images.

MATERIALS AND METHODS

Retrieved stroke thrombi were scanned ex vivo using a three-dimensional multi-echo gradient echo sequence and histologically analyzed. 188 thrombus R2*, quantitative susceptibility mapping and late-echo GRE magnitude image slices were used to train and test a 3-layer CNN through cross-validation. Data augmentation techniques involving input equalization and random image transformation were employed to improve network performance. The network was assessed for its ability to quantitatively predict RBC content and to classify thrombi into RBC-rich and RBC-poor groups.

RESULTS

The CNN predicted thrombus RBC content with an accuracy of 62% (95% CI 48-76%) when trained on the original dataset and improved to 72% (95% CI 60-84%) on the augmented dataset. The network classified thrombi as RBC-rich or poor with an accuracy of 71% (95% CI 58-84%) and an area under the curve of 0.72 (95% CI 0.57-0.87) when trained on the original dataset and improved to 80% (95% CI 69-91%) and 0.84 (95% CI 0.73-0.95), respectively, on the augmented dataset.

CONCLUSIONS

The CNN was able to accurately predict thrombus RBC content using multiparametric MR images, and could provide a means to guide treatment strategy in acute ischemic stroke.

Combination of optical coherence tomography-derived shape and texture features are associated with development of sub-foveal geographic atrophy in dry AMD

Geographic atrophy (GA) is an advanced form of dry age-related macular degeneration (AMD) that leads to progressive and irreversible vision loss. Identifying patients with greatest risk of GA progression is important for targeted utilization of emerging therapies. This study aimed to comprehensively evaluate the role of shape-based fractal dimension features ( F fd ) of sub-retinal pigment epithelium (sub-RPE) compartment and texture-based radiomics features ( F t ) of Ellipsoid Zone (EZ)-RPE and sub-RPE compartments for risk stratification for subfoveal GA (sfGA) progression. This was a retrospective study of 137 dry AMD subjects with a 5-year follow-up. Based on sfGA status at year 5, eyes were categorized as Progressors and Non-progressors. A total of 15 shape-based F fd of sub-RPE surface and 494 F t from each of sub-RPE and EZ-RPE compartments were extracted from baseline spectral domain-optical coherence tomography scans. The top nine features were identified from F fd and F t feature pool separately using minimum Redundancy maximum Relevance feature selection and used to train a Random Forest (RF) classifier independently using three-fold cross validation on the training set ( S t , N = 90) to distinguish between sfGA Progressors and Non-progressors. Combined F fd and F t was also evaluated in predicting risk of sfGA progression. The RF classifier yielded AUC of 0.85, 0.79 and 0.89 on independent test set ( S v , N = 47) using F fd , F t , and their combination, respectively. Using combined F fd and F t , the improvement in AUC was statistically significant on S v with p-values of 0.032 and 0.04 compared to using only F fd and only F t , respectively. Combined F fd and F t appears to identify high-risk patients. Our results show that FD and texture features could be potentially used for predicting risk of sfGA progression and future therapeutic response.

A user-friendly deep learning application for accurate lung cancer diagnosis

BACKGROUND

Accurate diagnosis and subsequent delineated treatment planning require the experience of clinicians in the handling of their case numbers. However, applying deep learning in image processing is useful in creating tools that promise faster high-quality diagnoses, but the accuracy and precision of 3-D image processing from 2-D data may be limited by factors such as superposition of organs, distortion and magnification, and detection of new pathologies. The purpose of this research is to use radiomics and deep learning to develop a tool for lung cancer diagnosis.

METHODS

This study applies radiomics and deep learning in the diagnosis of lung cancer to help clinicians accurately analyze the images and thereby provide the appropriate treatment planning. 86 patients were recruited from Bach Mai Hospital, and 1012 patients were collected from an open-source database. First, deep learning has been applied in the process of segmentation by U-NET and cancer classification via the use of the DenseNet model. Second, the radiomics were applied for measuring and calculating diameter, surface area, and volume. Finally, the hardware also was designed by connecting between Arduino Nano and MFRC522 module for reading data from the tag. In addition, the displayed interface was created on a web platform using Python through Streamlit.

RESULTS

The applied segmentation model yielded a validation loss of 0.498, a train loss of 0.27, a cancer classification validation loss of 0.78, and a training accuracy of 0.98. The outcomes of the diagnostic capabilities of lung cancer (recognition and classification of lung cancer from chest CT scans) were quite successful.

CONCLUSIONS

The model provided means for storing and updating patients' data directly on the interface which allowed the results to be readily available for the health care providers. The developed system will improve clinical communication and information exchange. Moreover, it can manage efforts by generating correlated and coherent summaries of cancer diagnoses.

Novel Fractal-Based Sub-RPE Compartment OCT Radiomics Biomarkers Are Associated With Subfoveal Geographic Atrophy in Dry AMD

OBJECTIVE

The purpose of this study was to quantitatively characterize the shape of the sub-retinal pigment epithelium (sub-RPE, i.e., space bounded by RPE and Bruch's membrane) compartment on SD-OCT using fractal dimension (FD) features and evaluate their impact on risk of subfoveal geographic atrophy (sfGA) progression.

METHODS

This was an IRB-approved retrospective study of 137 subjects with dry age-related macular degeneration (AMD) with subfoveal GA. Based on sfGA status at year five, eyes were categorized as "Progressors" and "Non-progressors". FD analysis allows quantification of the degree of shape complexity and architectural disorder associated with a structure. To characterize the structural irregularities along the sub-RPE surface between the two groups of patients, a total of 15 shape descriptors of FD were extracted from the sub-RPE compartment of baseline OCT scans. The top four features were identified using minimum Redundancy maximum Relevance (mRmR) feature selection method and evaluated with Random Forest (RF) classifier using three-fold cross validation from the training set (N = 90). Classifier performance was subsequently validated on the independent test set (N = 47).

RESULTS

Using the top four FD features, a RF classifier yielded an AUC of 0.85 on the independent test set. Mean fractal entropy (p-value = 4.8e-05) was identified as the most significant biomarker; higher values of entropy being associated with greater shape disorder and risk for sfGA progression.

CONCLUSIONS

FD assessment holds promise for identifying high-risk eyes for GA progression.

SIGNIFICANCE

With further validation, FD features could be potentially used for clinical trial enrichment and assessments for therapeutic response in dry AMD patients.

MRI-based nomograms and radiomics in presurgical prediction of extraprostatic extension in prostate cancer: a systematic review

PURPOSE

Prediction of extraprostatic extension (EPE) is essential for accurate surgical planning in prostate cancer (PCa). Radiomics based on magnetic resonance imaging (MRI) has shown potential to predict EPE. We aimed to evaluate studies proposing MRI-based nomograms and radiomics for EPE prediction and assess the quality of current radiomics literature.

METHODS

We used PubMed, EMBASE, and SCOPUS databases to find related articles using synonyms for MRI radiomics and nomograms to predict EPE. Two co-authors scored the quality of radiomics literature using the Radiomics Quality Score (RQS). Inter-rater agreement was measured using the intraclass correlation coefficient (ICC) from total RQS scores. We analyzed the characteristic s of the studies and used ANOVAs to associate the area under the curve (AUC) to sample size, clinical and imaging variables, and RQS scores.

RESULTS

We identified 33 studies-22 nomograms and 11 radiomics analyses. The mean AUC for nomogram articles was 0.783, and no significant associations were found between AUC and sample size, clinical variables, or number of imaging variables. For radiomics articles, there were significant associations between number of lesions and AUC (p < 0.013). The average RQS total score was 15.91/36 (44%). Through the radiomics operation, segmentation of region-of-interest, selection of features, and model building resulted in a broader range of results. The qualities the studies lacked most were phantom tests for scanner variabilities, temporal variability, external validation datasets, prospective designs, cost-effectiveness analysis, and open science.

CONCLUSION

Utilizing MRI-based radiomics to predict EPE in PCa patients demonstrates promising outcomes. However, quality improvement and standardization of radiomics workflow are needed.

The Use of MRI-Derived Radiomic Models in Prostate Cancer Risk Stratification: A Critical Review of Contemporary Literature

The development of precise medical imaging has facilitated the establishment of radiomics, a computer-based method of quantitatively analyzing subvisual imaging characteristics. The present review summarizes the current literature on the use of diagnostic magnetic resonance imaging (MRI)-derived radiomics in prostate cancer (PCa) risk stratification. A stepwise literature search of publications from 2017 to 2022 was performed. Of 218 articles on MRI-derived prostate radiomics, 33 (15.1%) generated models for PCa risk stratification. Prediction of Gleason score (GS), adverse pathology, postsurgical recurrence, and postradiation failure were the primary endpoints in 15 (45.5%), 11 (33.3%), 4 (12.1%), and 3 (9.1%) studies. In predicting GS and adverse pathology, radiomic models differentiated well, with receiver operator characteristic area under the curve (ROC-AUC) values of 0.50–0.92 and 0.60–0.92, respectively. For studies predicting post-treatment recurrence or failure, ROC-AUC for radiomic models ranged from 0.73 to 0.99 in postsurgical and radiation cohorts. Finally, of the 33 studies, 7 (21.2%) included external validation. Overall, most investigations showed good to excellent prediction of GS and adverse pathology with MRI-derived radiomic features. Direct prediction of treatment outcomes, however, is an ongoing investigation. As these studies mature and reach potential for clinical integration, concerted effort to validate these radiomic models must be undertaken.

Radiomics vs radiologist in prostate cancer. Results from a systematic review

PURPOSE

Radiomics in uro-oncology is a rapidly evolving science proving to be a novel approach for optimizing the analysis of massive data from medical images to provide auxiliary guidance in clinical issues. This scoping review aimed to identify key aspects wherein radiomics can potentially improve the accuracy of diagnosis, staging, and extraprostatic extension in prostate cancer (PCa).

METHODS

The literature search was performed on June 2022 using PubMed, Embase, and Cochrane Central Controlled Register of Trials. Studies were included if radiomics were compared with radiological reports only.

RESULTS

Seventeen papers were included. The combination of PIRADS and radiomics score models improves the PIRADS score reporting of 2 and 3 lesions even in the peripheral zone. Multiparametric MRI-based radiomics models suggest that by simply omitting diffusion contrast enhancement imaging in radiomics models can simplify the process of analysis of clinically significant PCa by PIRADS. Radiomics features correlated with the Gleason grade with excellent discriminative ability. Radiomics has higher accuracy in predicting not only the presence but also the side of extraprostatic extension.

CONCLUSIONS

Radiomics research on PCa mainly uses MRI as an imaging modality and is focused on diagnosis and risk stratification and has the best future possibility of improving PIRADS reporting. Radiomics has established its superiority over radiologist-reported outcomes but the variability has to be taken into consideration before translating it to clinical practice.

Radiomics-Based Assessment of OCT Angiography Images for Diabetic Retinopathy Diagnosis

Purpose

To evaluate the diagnostic accuracy of machine learning (ML) techniques applied to radiomic features extracted from OCT and OCT angiography (OCTA) images for diabetes mellitus (DM), diabetic retinopathy (DR), and referable DR (R-DR) diagnosis.

Design

Cross-sectional analysis of a retinal image dataset from a previous prospective OCTA study (ClinicalTrials.govNCT03422965).

Participants

Patients with type 1 DM and controls included in the progenitor study.

Methods

Radiomic features were extracted from fundus retinographies, OCT, and OCTA images in each study eye. Logistic regression, linear discriminant analysis, support vector classifier (SVC)-linear, SVC-radial basis function, and random forest models were created to evaluate their diagnostic accuracy for DM, DR, and R-DR diagnosis in all image types.

Main Outcome Measures

Area under the receiver operating characteristic curve (AUC) mean and standard deviation for each ML model and each individual and combined image types.

Results

A dataset of 726 eyes (439 individuals) were included. For DM diagnosis, the greatest AUC was observed for OCT (0.82, 0.03). For DR detection, the greatest AUC was observed for OCTA (0.77, 0.03), especially in the 3 × 3 mm superficial capillary plexus OCTA scan (0.76, 0.04). For R-DR diagnosis, the greatest AUC was observed for OCTA (0.87, 0.12) and the deep capillary plexus OCTA scan (0.86, 0.08). The addition of clinical variables (age, sex, etc.) improved most models AUC for DM, DR and R-DR diagnosis. The performance of the models was similar in unilateral and bilateral eyes image datasets.

Conclusions

Radiomics extracted from OCT and OCTA images allow identification of patients with DM, DR, and R-DR using standard ML classifiers. OCT was the best test for DM diagnosis, OCTA for DR and R-DR diagnosis and the addition of clinical variables improved most models. This pioneer study demonstrates that radiomics-based ML techniques applied to OCT and OCTA images may be an option for DR screening in patients with type 1 DM.

Financial Disclosures

Proprietary or commercial disclosure may be found after the references.

Quantib Prostate Compared to an Expert Radiologist for the Diagnosis of Prostate Cancer on mpMRI: A Single-Center Preliminary Study

Background: To evaluate the clinical utility of an Artificial Intelligence (AI) radiology solution, Quantib Prostate, for prostate cancer (PCa) lesions detection on multiparametric Magnetic Resonance Images (mpMRI). Methods: Prostate mpMRI exams of 108 patients were retrospectively studied. The diagnostic performance of an expert radiologist (>8 years of experience) and of an inexperienced radiologist aided by Quantib software were compared. Three groups of patients were assessed: patients with positive mpMRI, positive target biopsy, and/or at least one positive random biopsy (group A, 73 patients); patients with positive mpMRI and a negative biopsy (group B, 14 patients), and patients with negative mpMRI who did not undergo biopsy (group-C, 21 patients). Results: In group A, the AI-assisted radiologist found new lesions with positive biopsy correlation, increasing the diagnostic PCa performance when compared with the expert radiologist, reaching an SE of 92.3% and a PPV of 90.1% (vs. 71.7% and 84.4%). In group A, the expert radiologist found 96 lesions on 73 mpMRI exams (17.7% PIRADS3, 56.3% PIRADS4, and 26% PIRADS5). The AI-assisted radiologist found 121 lesions (0.8% PIRADS3, 53.7% PIRADS4, and 45.5% PIRADS5). At biopsy, 33.9% of the lesions were ISUP1, 31.4% were ISUP2, 22% were ISUP3, 10.2% were ISUP4, and 2.5% were ISUP5. In group B, where biopsies were negative, the AI-assisted radiologist excluded three lesions but confirmed all the others. In group-C, the AI-assisted radiologist found 37 new lesions, most of them PIRADS 3, with 32.4% localized in the peripherical zone and 67.6% in the transition zone. Conclusions: Quantib software is a very sensitive tool to use specifically in high-risk patients (high PIRADS and high Gleason score).

Role of Artificial Intelligence in Radiogenomics for Cancers in the Era of Precision Medicine

Simple Summary

Recently, radiogenomics has played a significant role and offered a new understanding of cancer’s biology and behavior in response to standard therapy. It also provides a more precise prognosis, investigation, and analysis of the patient’s cancer. Over the years, Artificial Intelligence (AI) has provided a significant strength in radiogenomics. In this paper, we offer computational and oncological prospects of the role of AI in radiogenomics, as well as its offers, achievements, opportunities, and limitations in the current clinical practices.

Abstract

Radiogenomics, a combination of “Radiomics” and “Genomics,” using Artificial Intelligence (AI) has recently emerged as the state-of-the-art science in precision medicine, especially in oncology care. Radiogenomics syndicates large-scale quantifiable data extracted from radiological medical images enveloped with personalized genomic phenotypes. It fabricates a prediction model through various AI methods to stratify the risk of patients, monitor therapeutic approaches, and assess clinical outcomes. It has recently shown tremendous achievements in prognosis, treatment planning, survival prediction, heterogeneity analysis, reoccurrence, and progression-free survival for human cancer study. Although AI has shown immense performance in oncology care in various clinical aspects, it has several challenges and limitations. The proposed review provides an overview of radiogenomics with the viewpoints on the role of AI in terms of its promises for computational as well as oncological aspects and offers achievements and opportunities in the era of precision medicine. The review also presents various recommendations to diminish these obstacles.

RADIomic Spatial TexturAl descripTor (RADISTAT): Quantifying spatial organization of imaging heterogeneity associated with tumor response to treatment

Localized disease heterogeneity on imaging extracted via radiomics approaches have recently been associated with disease prognosis and treatment response. Traditionally, radiomics analyses leverage texture operators to derive voxel- or region-wise feature values towards quantifying subtle variations in image appearance within a region-of-interest (ROI). With the goal of mining additional voxel-wise texture patterns from radiomic expression maps, we introduce a new RADIomic Spatial TexturAl descripTor (RADISTAT). This was driven by the hypothesis that quantifying spatial organization of texture patterns within an ROI could allow for better capturing interactions between different tissue classes present in a given region; thus enabling more accurate characterization of disease or response phenotypes. RADISTAT involves: (a) robustly identifying sub-compartments of low, intermediate, and high radiomic expression (i.e. heterogeneity) in a feature map and (b) quantifying spatial organization of sub-compartments via graph interactions. RADISTAT was evaluated in two clinically challenging problems: (1) discriminating nodal/distant metastasis from metastasis-free rectal cancer patients on post-chemoradiation T2w MRI, and (2) distinguishing tumor progression from pseudo-progression in glioblastoma multiforme using post-chemoradiation T1w MRI. Across over 800 experiments, RADISTAT yielded a consistent discriminatory signature for tumor progression (GBM) and disease metastasis (RCa); where its sub-compartments were associated with pathologic tissue types (fibrosis or tumor, determined via fusion of MRI and pathology). In a multi-institutional setting for both clinical problems, RADISTAT resulted in higher classifier performance (11% improvement in AUC, on average) compared to radiomic descriptors. Furthermore, combining RADISTAT with radiomic descriptors resulted in significantly improved performance compared to using radiomic descriptors alone.

Machine and Deep Learning Prediction Of Prostate Cancer Aggressiveness Using Multiparametric MRI

Prostate cancer (PCa) is the most frequent male malignancy and the assessment of PCa aggressiveness, for which a biopsy is required, is fundamental for patient management. Currently, multiparametric (mp) MRI is strongly recommended before biopsy. Quantitative assessment of mpMRI might provide the radiologist with an objective and noninvasive tool for supporting the decision-making in clinical practice and decreasing intra- and inter-reader variability. In this view, high dimensional radiomics features and Machine Learning (ML) techniques, along with Deep Learning (DL) methods working on raw images directly, could assist the radiologist in the clinical workflow. The aim of this study was to develop and validate ML/DL frameworks on mpMRI data to characterize PCas according to their aggressiveness. We optimized several ML/DL frameworks on T2w, ADC and T2w+ADC data, using a patient-based nested validation scheme. The dataset was composed of 112 patients (132 peripheral lesions with Prostate Imaging Reporting and Data System (PI-RADS) score ≥ 3) acquired following both PI-RADS 2.0 and 2.1 guidelines. Firstly, ML/DL frameworks trained and validated on PI-RADS 2.0 data were tested on both PI-RADS 2.0 and 2.1 data. Then, we trained, validated and tested ML/DL frameworks on a multi PI-RADS dataset. We reported the performances in terms of Area Under the Receiver Operating curve (AUROC), specificity and sensitivity. The ML/DL frameworks trained on T2w data achieved the overall best performance. Notably, ML and DL frameworks trained and validated on PI-RADS 2.0 data obtained median AUROC values equal to 0.750 and 0.875, respectively, on unseen PI-RADS 2.0 test set. Similarly, ML/DL frameworks trained and validated on multi PI-RADS T2w data showed median AUROC values equal to 0.795 and 0.750, respectively, on unseen multi PI-RADS test set. Conversely, all the ML/DL frameworks trained and validated on PI-RADS 2.0 data, achieved AUROC values no better than the chance level when tested on PI-RADS 2.1 data. Both ML/DL techniques applied on mpMRI seem to be a valid aid in predicting PCa aggressiveness. In particular, ML/DL frameworks fed with T2w images data (objective, fast and non-invasive) show good performances and might support decision-making in patient diagnostic and therapeutic management, reducing intra- and inter-reader variability.

Radiomics in prostate cancer: an up-to-date review

Prostate cancer (PCa) is the most common worldwide diagnosed malignancy in male population. The diagnosis, the identification of aggressive disease, and the post-treatment follow-up needs a more comprehensive and holistic approach. Radiomics is the extraction and interpretation of images phenotypes in a quantitative manner. Radiomics may give an advantage through advancements in imaging modalities and through the potential power of artificial intelligence techniques by translating those features into clinical outcome prediction. This article gives an overview on the current evidence of methodology and reviews the available literature on radiomics in PCa patients, highlighting its potential for personalized treatment and future applications.

Selective identification and localization of indolent and aggressive prostate cancers via CorrSigNIA: an MRI-pathology correlation and deep learning framework

Automated methods for detecting prostate cancer and distinguishing indolent from aggressive disease on Magnetic Resonance Imaging (MRI) could assist in early diagnosis and treatment planning. Existing automated methods of prostate cancer detection mostly rely on ground truth labels with limited accuracy, ignore disease pathology characteristics observed on resected tissue, and cannot selectively identify aggressive (Gleason Pattern≥4) and indolent (Gleason Pattern=3) cancers when they co-exist in mixed lesions. In this paper, we present a radiology-pathology fusion approach, CorrSigNIA, for the selective identification and localization of indolent and aggressive prostate cancer on MRI. CorrSigNIA uses registered MRI and whole-mount histopathology images from radical prostatectomy patients to derive accurate ground truth labels and learn correlated features between radiology and pathology images. These correlated features are then used in a convolutional neural network architecture to detect and localize normal tissue, indolent cancer, and aggressive cancer on prostate MRI. CorrSigNIA was trained and validated on a dataset of 98 men, including 74 men that underwent radical prostatectomy and 24 men with normal prostate MRI. CorrSigNIA was tested on three independent test sets including 55 men that underwent radical prostatectomy, 275 men that underwent targeted biopsies, and 15 men with normal prostate MRI. CorrSigNIA achieved an accuracy of 80% in distinguishing between men with and without cancer, a lesion-level ROC-AUC of 0.81±0.31 in detecting cancers in both radical prostatectomy and biopsy cohort patients, and lesion-levels ROC-AUCs of 0.82±0.31 and 0.86±0.26 in detecting clinically significant cancers in radical prostatectomy and biopsy cohort patients respectively. CorrSigNIA consistently outperformed other methods across different evaluation metrics and cohorts. In clinical settings, CorrSigNIA may be used in prostate cancer detection as well as in selective identification of indolent and aggressive components of prostate cancer, thereby improving prostate cancer care by helping guide targeted biopsies, reducing unnecessary biopsies, and selecting and planning treatment.

Quantitative Imaging Biomarkers in Age-Related Macular Degeneration and Diabetic Eye Disease: A Step Closer to Precision Medicine

The management of retinal diseases relies heavily on digital imaging data, including optical coherence tomography (OCT) and fluorescein angiography (FA). Targeted feature extraction and the objective quantification of features provide important opportunities in biomarker discovery, disease burden assessment, and predicting treatment response. Additional important advantages include increased objectivity in interpretation, longitudinal tracking, and ability to incorporate computational models to create automated diagnostic and clinical decision support systems. Advances in computational technology, including deep learning and radiomics, open new doors for developing an imaging phenotype that may provide in-depth personalized disease characterization and enhance opportunities in precision medicine. In this review, we summarize current quantitative and radiomic imaging biomarkers described in the literature for age-related macular degeneration and diabetic eye disease using imaging modalities such as OCT, FA, and OCT angiography (OCTA). Various approaches used to identify and extract these biomarkers that utilize artificial intelligence and deep learning are also summarized in this review. These quantifiable biomarkers and automated approaches have unleashed new frontiers of personalized medicine where treatments are tailored, based on patient-specific longitudinally trackable biomarkers, and response monitoring can be achieved with a high degree of accuracy.

Integrating pathomics with radiomics and genomics for cancer prognosis: A brief review

In the last decade, the focus of computational pathology research community has shifted from replicating the pathological examination for diagnosis done by pathologists to unlocking and discovering "sub-visual" prognostic image cues from the histopathological image. While we are getting more knowledge and experience in digital pathology, the emerging goal is to integrate other-omics or modalities that will contribute for building a better prognostic assay. In this paper, we provide a brief review of representative works that focus on integrating pathomics with radiomics and genomics for cancer prognosis. It includes: correlation of pathomics and genomics; fusion of pathomics and genomics; fusion of pathomics and radiomics. We also present challenges, potential opportunities, and avenues for future work.

Machine Learning: Applications and Advanced Progresses of Radiomics in Endocrine Neoplasms

Endocrine neoplasms remain a great threat to human health. It is extremely important to make a clear diagnosis and timely treatment of endocrine tumors. Machine learning includes radiomics, which has long been utilized in clinical cancer research. Radiomics refers to the extraction of valuable information by analyzing a large amount of standard data with high-throughput medical images mainly including computed tomography, positron emission tomography, magnetic resonance imaging, and ultrasound. With the quantitative imaging analysis and model building, radiomics can reflect specific underlying characteristics of a disease that otherwise could not be evaluated visually. More and more promising results of radiomics in oncological practice have been seen in recent years. Radiomics may have the potential to supplement traditional imaging analysis and assist in providing precision medicine for patients. Radiomics had developed rapidly in endocrine neoplasms practice in the past decade. In this review, we would introduce the general workflow of radiomics and summarize the applications and developments of radiomics in endocrine neoplasms in recent years. The limitations of current radiomic research studies and future development directions would also be discussed.

Prostate Cancer Radiogenomics-From Imaging to Molecular Characterization

Radiomics and genomics represent two of the most promising fields of cancer research, designed to improve the risk stratification and disease management of patients with prostate cancer (PCa). Radiomics involves a conversion of imaging derivate quantitative features using manual or automated algorithms, enhancing existing data through mathematical analysis. This could increase the clinical value in PCa management. To extract features from imaging methods such as magnetic resonance imaging (MRI), the empiric nature of the analysis using machine learning and artificial intelligence could help make the best clinical decisions. Genomics information can be explained or decoded by radiomics. The development of methodologies can create more-efficient predictive models and can better characterize the molecular features of PCa. Additionally, the identification of new imaging biomarkers can overcome the known heterogeneity of PCa, by non-invasive radiological assessment of the whole specific organ. In the future, the validation of recent findings, in large, randomized cohorts of PCa patients, can establish the role of radiogenomics. Briefly, we aimed to review the current literature of highly quantitative and qualitative results from well-designed studies for the diagnoses, treatment, and follow-up of prostate cancer, based on radiomics, genomics and radiogenomics research.

Incorporating radiomics into clinical trials: expert consensus endorsed by the European Society of Radiology on considerations for data-driven compared to biologically driven quantitative biomarkers

Existing quantitative imaging biomarkers (QIBs) are associated with known biological tissue characteristics and follow a well-understood path of technical, biological and clinical validation before incorporation into clinical trials. In radiomics, novel data-driven processes extract numerous visually imperceptible statistical features from the imaging data with no a priori assumptions on their correlation with biological processes. The selection of relevant features (radiomic signature) and incorporation into clinical trials therefore requires additional considerations to ensure meaningful imaging endpoints. Also, the number of radiomic features tested means that power calculations would result in sample sizes impossible to achieve within clinical trials. This article examines how the process of standardising and validating data-driven imaging biomarkers differs from those based on biological associations. Radiomic signatures are best developed initially on datasets that represent diversity of acquisition protocols as well as diversity of disease and of normal findings, rather than within clinical trials with standardised and optimised protocols as this would risk the selection of radiomic features being linked to the imaging process rather than the pathology. Normalisation through discretisation and feature harmonisation are essential pre-processing steps. Biological correlation may be performed after the technical and clinical validity of a radiomic signature is established, but is not mandatory. Feature selection may be part of discovery within a radiomics-specific trial or represent exploratory endpoints within an established trial; a previously validated radiomic signature may even be used as a primary/secondary endpoint, particularly if associations are demonstrated with specific biological processes and pathways being targeted within clinical trials. KEY POINTS: • Data-driven processes like radiomics risk false discoveries due to high-dimensionality of the dataset compared to sample size, making adequate diversity of the data, cross-validation and external validation essential to mitigate the risks of spurious associations and overfitting. • Use of radiomic signatures within clinical trials requires multistep standardisation of image acquisition, image analysis and data mining processes. • Biological correlation may be established after clinical validation but is not mandatory.

Multi-Compartment Spatially-Derived Radiomics From Optical Coherence Tomography Predict Anti-VEGF Treatment Durability in Macular Edema Secondary to Retinal Vascular Disease: Preliminary Findings

OBJECTIVE

Diabetic macular edema (DME) and retinal vein occlusion (RVO) are the leading causes of visual impairments across the world. Vascular endothelial growth factor (VEGF) stimulates breakdown of blood-retinal barrier that causes accumulation of fluid within macula. Anti-VEGF therapy is the first-line treatment for both the diseases; however, the degree of response varies for individual patients. The main objective of this work was to identify the (i) texture-based radiomics features within individual fluid and retinal tissue compartments of baseline spectral-domain optical coherence tomography (SD-OCT) images and (ii) the specific spatial compartments that contribute most pertinent features for predicting therapeutic response.

METHODS

A total of 962 texture-based radiomics features were extracted from each of the fluid and retinal tissue compartments of OCT images, obtained from the PERMEATE study. Top-performing features selected from the consensus of different feature selection methods were evaluated in conjunction with four different machine learning classifiers: Linear Discriminant Analysis (LDA), Quadratic Discriminant Analysis (QDA), Random Forest (RF), and Support Vector Machine (SVM) in a cross-validated approach to distinguish eyes tolerating extended interval dosing (non-rebounders) and those requiring more frequent dosing (rebounders).

RESULTS

Combination of fluid and retinal tissue features yielded a cross-validated area under receiver operating characteristic curve (AUC) of 0.78±0.08 in distinguishing rebounders from non-rebounders.

CONCLUSIONS

This study revealed that the texture-based radiomics features pertaining to IRF subcompartment were most discriminating between rebounders and non-rebounders to anti-VEGF therapy. Clinical Impact: With further validation, OCT-based imaging biomarkers could be used for treatment management of DME patients.

Radiomics in prostate cancer imaging for a personalized treatment approach - current aspects of methodology and a systematic review on validated studies

Prostate cancer (PCa) is one of the most frequently diagnosed malignancies of men in the world. Due to a variety of treatment options in different risk groups, proper diagnostic and risk stratification is pivotal in treatment of PCa. The development of precise medical imaging procedures simultaneously to improvements in big data analysis has led to the establishment of radiomics - a computer-based method of extracting and analyzing image features quantitatively. This approach bears the potential to assess and improve PCa detection, tissue characterization and clinical outcome prediction. This article gives an overview on the current aspects of methodology and systematically reviews available literature on radiomics in PCa patients, showing its potential for personalized therapy approaches. The qualitative synthesis includes all imaging modalities and focuses on validated studies, putting forward future directions.

MRI-based radiomics models to assess prostate cancer, extracapsular extension and positive surgical margins

Purpose

To investigate the performance of magnetic resonance imaging (MRI)-based radiomics models for benign and malignant prostate lesion discrimination and extracapsular extension (ECE) and positive surgical margins (PSM) prediction.

Methods and materials

In total, 459 patients who underwent multiparametric MRI (mpMRI) before prostate biopsy were included. Radiomic features were extracted from both T2-weighted imaging (T2WI) and the apparent diffusion coefficient (ADC). Patients were divided into different training sets and testing sets for different targets according to a ratio of 7:3. Radiomics signatures were built using radiomic features on the training set, and integrated models were built by adding clinical characteristics. The areas under the receiver operating characteristic curves (AUCs) were calculated to assess the classification performance on the testing sets.

Results

The radiomics signatures for benign and malignant lesion discrimination achieved AUCs of 0.775 (T2WI), 0.863 (ADC) and 0.855 (ADC + T2WI). The corresponding integrated models improved the AUC to 0.851/0.912/0.905, respectively. The radiomics signatures for ECE achieved the highest AUC of 0.625 (ADC), and the corresponding integrated model achieved the highest AUC (0.728). The radiomics signatures for PSM prediction achieved AUCs of 0.614 (T2WI) and 0.733 (ADC). The corresponding integrated models reached AUCs of 0.680 and 0.766, respectively.

Conclusions

The MRI-based radiomics models, which took advantage of radiomic features on ADC and T2WI scans, showed good performance in discriminating benign and malignant prostate lesions and predicting ECE and PSM. Combining radiomics signatures and clinical factors enhanced the performance of the models, which may contribute to clinical diagnosis and treatment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40644-021-00414-6.

Characterisation of prostate cancer using texture analysis for diagnostic and prognostic monitoring

Automated classification of significant prostate cancer (PCa) using MRI plays a potential role in assisting in clinical decision-making. Multiparametric MRI using a machine-aided approach is a better step to improve the overall accuracy of diagnosis of PCa. The objective of this study was to develop and validate a framework for differentiating Prostate Imaging-Reporting and Data System version 2 (PI-RADS v2) grades (grade 2 to grade 5) of PCa using texture features and machine learning (ML) methods with diffusion-weighted imaging (DWI) and apparent diffusion coefficient (ADC). The study cohort included an MRI dataset of 59 patients with clinically proven PCa. Regions of interest (ROIs) for a total of 435 lesions were delineated from the segmented peripheral zones of DWI and ADC. Six texture methods comprising 98 texture features in total (49 each of DWI and ADC) were extracted from lesion ROIs. Random forest (RF) and correlation-based feature selection methods were applied on feature vectors to select the best features for classification. Two ML classifiers, support vector machine (SVM) and K-nearest neighbour, were used and validated by 10-fold cross-validation. The proposed framework achieved high diagnostic performance with a sensitivity of 85.25% ± 3.84%, specificity of 95.71% ± 1.96%, accuracy of 84.90% ± 3.37% and area under the receiver-operating characteristic curve of 0.98 for PI-RADS v2 grades (2 to 5) classification using the RF feature selection method and Gaussian SVM classifier with combined features of DWI + ADC. The proposed computer-assisted framework can distinguish between PCa lesions with different aggressiveness based on PI-RADS v2 standards using texture analysis to improve the efficiency of PCa diagnostic performance.

Deep learning classification of lung cancer histology using CT images

Tumor histology is an important predictor of therapeutic response and outcomes in lung cancer. Tissue sampling for pathologist review is the most reliable method for histology classification, however, recent advances in deep learning for medical image analysis allude to the utility of radiologic data in further describing disease characteristics and for risk stratification. In this study, we propose a radiomics approach to predicting non-small cell lung cancer (NSCLC) tumor histology from non-invasive standard-of-care computed tomography (CT) data. We trained and validated convolutional neural networks (CNNs) on a dataset comprising 311 early-stage NSCLC patients receiving surgical treatment at Massachusetts General Hospital (MGH), with a focus on the two most common histological types: adenocarcinoma (ADC) and Squamous Cell Carcinoma (SCC). The CNNs were able to predict tumor histology with an AUC of 0.71(p = 0.018). We also found that using machine learning classifiers such as k-nearest neighbors (kNN) and support vector machine (SVM) on CNN-derived quantitative radiomics features yielded comparable discriminative performance, with AUC of up to 0.71 (p = 0.017). Our best performing CNN functioned as a robust probabilistic classifier in heterogeneous test sets, with qualitatively interpretable visual explanations to its predictions. Deep learning based radiomics can identify histological phenotypes in lung cancer. It has the potential to augment existing approaches and serve as a corrective aid for diagnosticians.

Harnessing non-destructive 3D pathology

High-throughput methods for slide-free three-dimensional (3D) pathological analyses of whole biopsies and surgical specimens offer the promise of modernizing traditional histology workflows and delivering improvements in diagnostic performance. Advanced optical methods now enable the interrogation of orders of magnitude more tissue than previously possible, where volumetric imaging allows for enhanced quantitative analyses of cell distributions and tissue structures that are prognostic and predictive. Non-destructive imaging processes can simplify laboratory workflows, potentially reducing costs, and can ensure that samples are available for subsequent molecular assays. However, the large size of the feature-rich datasets that they generate poses challenges for data management and computer-aided analysis. In this Perspective, we provide an overview of the imaging technologies that enable 3D pathology, and the computational tools-machine learning, in particular-for image processing and interpretation. We also discuss the integration of various other diagnostic modalities with 3D pathology, along with the challenges and opportunities for clinical adoption and regulatory approval.

A Multi-Center, Multi-Vendor Study to Evaluate the Generalizability of a Radiomics Model for Classifying Prostate cancer: High Grade vs. Low Grade

Radiomics applied in MRI has shown promising results in classifying prostate cancer lesions. However, many papers describe single-center studies without external validation. The issues of using radiomics models on unseen data have not yet been sufficiently addressed. The aim of this study is to evaluate the generalizability of radiomics models for prostate cancer classification and to compare the performance of these models to the performance of radiologists. Multiparametric MRI, photographs and histology of radical prostatectomy specimens, and pathology reports of 107 patients were obtained from three healthcare centers in the Netherlands. By spatially correlating the MRI with histology, 204 lesions were identified. For each lesion, radiomics features were extracted from the MRI data. Radiomics models for discriminating high-grade (Gleason score ≥ 7) versus low-grade lesions were automatically generated using open-source machine learning software. The performance was tested both in a single-center setting through cross-validation and in a multi-center setting using the two unseen datasets as external validation. For comparison with clinical practice, a multi-center classifier was tested and compared with the Prostate Imaging Reporting and Data System version 2 (PIRADS v2) scoring performed by two expert radiologists. The three single-center models obtained a mean AUC of 0.75, which decreased to 0.54 when the model was applied to the external data, the radiologists obtained a mean AUC of 0.46. In the multi-center setting, the radiomics model obtained a mean AUC of 0.75 while the radiologists obtained a mean AUC of 0.47 on the same subset. While radiomics models have a decent performance when tested on data from the same center(s), they may show a significant drop in performance when applied to external data. On a multi-center dataset our radiomics model outperformed the radiologists, and thus, may represent a more accurate alternative for malignancy prediction.

Radiomics and Prostate MRI: Current Role and Future Applications

Multiparametric prostate magnetic resonance imaging (mpMRI) is widely used as a triage test for men at a risk of prostate cancer. However, the traditional role of mpMRI was confined to prostate cancer staging. Radiomics is the quantitative extraction and analysis of minable data from medical images; it is emerging as a promising tool to detect and categorize prostate lesions. In this paper we review the role of radiomics applied to prostate mpMRI in detection and localization of prostate cancer, prediction of Gleason score and PI-RADS classification, prediction of extracapsular extension and of biochemical recurrence. We also provide a future perspective of artificial intelligence (machine learning and deep learning) applied to the field of prostate cancer.

A novel imaging based Nomogram for predicting post-surgical biochemical recurrence and adverse pathology of prostate cancer from pre-operative bi-parametric MRI

Background

We developed and validated an integrated radiomic-clinicopathologic nomogram (RadClip) for post-surgical biochemical recurrence free survival (bRFS) and adverse pathology (AP) prediction in men with prostate cancer (PCa). RadClip was further compared against extant prognostics tools like CAPRA and Decipher.

Methods

A retrospective study of 198 patients with PCa from four institutions who underwent pre-operative 3 Tesla MRI followed by radical prostatectomy, between 2009 and 2017 with a median 35-month follow-up was performed. Radiomic features were extracted from prostate cancer regions on bi-parametric magnetic resonance imaging (bpMRI). Cox Proportional-Hazards (CPH) model warped with minimum redundancy maximum relevance (MRMR) feature selection was employed to select bpMRI radiomic features for bRFS prediction in the training set (D₁, N = 71). In addition, a bpMRI radiomic risk score (RadS) and associated nomogram, RadClip, were constructed in D₁ and then compared against the Decipher, pre-operative (CAPRA), and post-operative (CAPRA-S) nomograms for bRFS and AP prediction in the testing set (D₂, N = 127).

Findings

“RadClip yielded a higher C-index (0.77, 95% CI 0.65-0.88) compared to CAPRA (0.68, 95% CI 0.57-0.8) and Decipher (0.51, 95% CI 0.33-0.69) and was found to be comparable to CAPRA-S (0.75, 95% CI 0.65-0.85). RadClip resulted in a higher AUC (0.71, 95% CI 0.62-0.81) for predicting AP compared to Decipher (0.66, 95% CI 0.56-0.77) and CAPRA (0.69, 95% CI 0.59-0.79).”

Interpretation

RadClip was more prognostic of bRFS and AP compared to Decipher and CAPRA. It could help pre-operatively identify PCa patients at low risk of biochemical recurrence and AP and who therefore might defer additional therapy.

Funding

The National Institutes of Health, the U.S. Department of Veterans Affairs, and the Department of Defense.

Identifying Cross-Scale Associations between Radiomic and Pathomic Signatures of Non-Small Cell Lung Cancer Subtypes: Preliminary Results

(1) Background: Despite the complementarity between radiology and histopathology, both from a diagnostic and a prognostic perspective, quantitative analyses of these modalities are usually performed in disconnected silos. This work presents initial results for differentiating two major non-small cell lung cancer (NSCLC) subtypes by exploring cross-scale associations between Computed Tomography (CT) images and corresponding digitized pathology images. (2) Methods: The analysis comprised three phases, (i) a multi-resolution cell density quantification to identify discriminant pathomic patterns for differentiating adenocarcinoma (ADC) and squamous cell carcinoma (SCC), (ii) radiomic characterization of CT images by using Haralick descriptors to quantify tumor textural heterogeneity as represented by gray-level co-occurrences to discriminate the two pathological subtypes, and (iii) quantitative correlation analysis between the multi-modal features to identify potential associations between them. This analysis was carried out using two publicly available digitized pathology databases (117 cases from TCGA and 54 cases from CPTAC) and a public radiological collection of CT images (101 cases from NSCLC-R). (3) Results: The top-ranked cell density pathomic features from the histopathology analysis were correlation, contrast, homogeneity, sum of entropy and difference of variance; which yielded a cross-validated AUC of 0.72 ± 0.02 on the training set (CPTAC) and hold-out validation AUC of 0.77 on the testing set (TCGA). Top-ranked co-occurrence radiomic features within NSCLC-R were contrast, correlation and sum of entropy which yielded a cross-validated AUC of 0.72 ± 0.01. Preliminary but significant cross-scale associations were identified between cell density statistics and CT intensity values using matched specimens available in the TCGA cohort, which were used to significantly improve the overall discriminatory performance of radiomic features in differentiating NSCLC subtypes (AUC = 0.78 ± 0.01). (4) Conclusions: Initial results suggest that cross-scale associations may exist between digital pathology and CT imaging which can be used to identify relevant radiomic and histopathology features to accurately distinguish lung adenocarcinomas from squamous cell carcinomas.

Introduction to radiomics and radiogenomics in neuro-oncology: implications and challenges

Neuro-oncology largely consists of malignancies of the brain and central nervous system including both primary as well as metastatic tumors. Currently, a significant clinical challenge in neuro-oncology is to tailor therapies for patients based on a priori knowledge of their survival outcome or treatment response to conventional or experimental therapies. Radiomics or the quantitative extraction of subvisual data from conventional radiographic imaging has recently emerged as a powerful data-driven approach to offer insights into clinically relevant questions related to diagnosis, prediction, prognosis, as well as assessing treatment response. Furthermore, radiogenomic approaches provide a mechanism to establish statistical correlations of radiomic features with point mutations and next-generation sequencing data to further leverage the potential of routine MRI scans to serve as "virtual biopsy" maps. In this review, we provide an introduction to radiomic and radiogenomic approaches in neuro-oncology, including a brief description of the workflow involving preprocessing, tumor segmentation, and extraction of "hand-crafted" features from the segmented region of interest, as well as identifying radiogenomic associations that could ultimately lead to the development of reliable prognostic and predictive models in neuro-oncology applications. Lastly, we discuss the promise of radiomics and radiogenomic approaches in personalizing treatment decisions in neuro-oncology, as well as the challenges with clinical adoption, which will rely heavily on their demonstrated resilience to nonstandardization in imaging protocols across sites and scanners, as well as in their ability to demonstrate reproducibility across large multi-institutional cohorts.

Radiomic Features of Primary Rectal Cancers on Baseline T2 -Weighted MRI Are Associated With Pathologic Complete Response to Neoadjuvant Chemoradiation: A Multisite Study

BACKGROUND

Twenty-five percent of rectal adenocarcinoma patients achieve pathologic complete response (pCR) to neoadjuvant chemoradiation and could avoid proctectomy. However, pretreatment clinical or imaging markers are lacking in predicting response to chemoradiation. Radiomic texture features from MRI have recently been associated with therapeutic response in other cancers.

PURPOSE

To construct a radiomics texture model based on pretreatment MRI for identifying patients who will achieve pCR to neoadjuvant chemoradiation in rectal cancer, including validation across multiple scanners and sites.

STUDY TYPE

Retrospective.

SUBJECTS

In all, 104 rectal cancer patients staged with MRI prior to long-course chemoradiation followed by proctectomy; curated from three institutions.

FIELD STRENGTH/SEQUENCE

1.5T-3.0T, axial higher resolution T2 -weighted turbo spin echo sequence.

ASSESSMENT

Pathologic response was graded on postsurgical specimens. In total, 764 radiomic features were extracted from single-slice sections of rectal tumors on processed pretreatment T2 -weighted MRI.

STATISTICAL TESTS

Three feature selection schemes were compared for identifying radiomic texture descriptors associated with pCR via a discovery cohort (one site, N = 60, cross-validation). The top-selected radiomic texture features were used to train and validate a random forest classifier model for pretreatment identification of pCR (two external sites, N = 44). Model performance was evaluated via area under the curve (AUC), accuracy, sensitivity, and specificity.

RESULTS

Laws kernel responses and gradient organization features were most associated with pCR (P ≤ 0.01); as well as being commonly identified across all feature selection schemes. The radiomics model yielded a discovery AUC of 0.699 ± 0.076 and a hold-out validation AUC of 0.712 with 70.5% accuracy (70.0% sensitivity, 70.6% specificity) in identifying pCR. Radiomic texture features were resilient to variations in magnetic field strength as well as being consistent between two different expert annotations. Univariate analysis revealed no significant associations of baseline clinicopathologic or MRI findings with pCR (P = 0.07-0.96).

DATA CONCLUSION

Radiomic texture features from pretreatment MRIs may enable early identification of potential pCR to neoadjuvant chemoradiation, as well as generalize across sites.

LEVEL OF EVIDENCE

3 TECHNICAL EFFICACY STAGE: 2.

Tumor Habitat-derived Radiomic Features at Pretreatment MRI That Are Prognostic for Progression-free Survival in Glioblastoma Are Associated with Key Morphologic Attributes at Histopathologic Examination: A Feasibility Study

PURPOSE

To identify radiomic features extracted from the tumor habitat on routine MR images that are prognostic for progression-free survival (PFS) and to assess their morphologic basis with corresponding histopathologic attributes in glioblastoma (GBM).

MATERIALS AND METHODS

In this retrospective study, 156 pretreatment GBM MR images (gadolinium-enhanced T1-weighted, T2-weighted, and fluid-attenuated inversion recovery [FLAIR] images) were curated. Of these 156 images, 122 were used for training (90 from The Cancer Imaging Archive and 32 from the Cleveland Clinic, acquired between December 1, 2011, and May 1, 2018) and 34 were used for validation. The validation set was obtained from the Ivy Glioblastoma Atlas Project database, for which the percentage extent of 11 histologic attributes was available on corresponding histopathologic specimens of the resected tumor. Following expert annotations of the tumor habitat (necrotic core, enhancing tumor, and FLAIR-hyperintense subcompartments), 1008 radiomic descriptors (eg, Haralick texture features, Laws energy features, co-occurrence of local anisotropic gradient orientations [CoLIAGe]) were extracted from the three MRI sequences. The top radiomic features were obtained from each subcompartment in the training set on the basis of their ability to risk-stratify patients according to PFS. These features were then concatenated to create a radiomics risk score (RRS). The RRS was independently validated on a holdout set. In addition, correlations (P < .05) of RRS features were computed, with the percentage extent of the 11 histopathologic attributes, using Spearman correlation analysis.

RESULTS

RRS yielded a concordance index of 0.80 on the validation set and constituted radiomic features, including Laws (capture edges, waves, ripple patterns) and CoLIAGe (capture disease heterogeneity) from enhancing tumor and FLAIR hyperintensity. These radiomic features were correlated with histopathologic attributes associated with disease aggressiveness in GBM, particularly tumor infiltration (P = .0044) and hyperplastic blood vessels (P = .0005).

CONCLUSION

Preliminary findings demonstrated significant associations of prognostic radiomic features with disease-specific histologic attributes, with implications for risk-stratifying patients with GBM for personalized treatment decisions. Supplemental material is available for this article. © RSNA, 2020.

How can we combat multicenter variability in MR radiomics? Validation of a correction procedure

OBJECTIVE

Test a practical realignment approach to compensate the technical variability of MR radiomic features.

METHODS

T1 phantom images acquired on 2 scanners, FLAIR and contrast-enhanced T1-weighted (CE-T1w) images of 18 brain tumor patients scanned on both 1.5-T and 3-T scanners, and 36 T2-weighted (T2w) images of prostate cancer patients scanned in one of two centers were investigated. The ComBat procedure was used for harmonizing radiomic features. Differences in statistical distributions in feature values between 1.5- and 3-T images were tested before and after harmonization. The prostate studies were used to determine the impact of harmonization to distinguish between Gleason grades (GGs).

RESULTS

In the phantom data, 40 out of 42 radiomic feature values were significantly different between the 2 scanners before harmonization and none after. In white matter regions, the statistical distributions of features were significantly different (p < 0.05) between the 1.5- and 3-T images for 37 out of 42 features in both FLAIR and CE-T1w images. After harmonization, no statistically significant differences were observed. In brain tumors, 41 (FLAIR) or 36 (CE-T1w) out of 42 features were significantly different between the 1.5- and 3-T images without harmonization, against 1 (FLAIR) or none (CE-T1w) with harmonization. In prostate studies, 636 radiomic features were significantly different between GGs after harmonization against 461 before. The ability to distinguish between GGs using radiomic features was increased after harmonization.

CONCLUSION

ComBat harmonization efficiently removes inter-center technical inconsistencies in radiomic feature values and increases the sensitivity of studies using data from several scanners.

KEY POINTS

• Radiomic feature values obtained using different MR scanners or imaging protocols can be harmonized by combining off-the-shelf image standardization and feature realignment procedures. • Harmonized radiomic features enable one to pool data from different scanners and centers without a substantial loss of statistical power caused by intra- and inter-center variability. • The proposed realignment method is applicable to radiomic features from different MR sequences and tumor types and does not rely on any phantom acquisition.

T1 and T2 MR fingerprinting measurements of prostate cancer and prostatitis correlate with deep learning-derived estimates of epithelium, lumen, and stromal composition on corresponding whole mount histopathology

OBJECTIVES

To explore the associations between T1 and T2 magnetic resonance fingerprinting (MRF) measurements and corresponding tissue compartment ratios (TCRs) on whole mount histopathology of prostate cancer (PCa) and prostatitis.

MATERIALS AND METHODS

A retrospective, IRB-approved, HIPAA-compliant cohort consisting of 14 PCa patients who underwent 3 T multiparametric MRI along with T1 and T2 MRF maps prior to radical prostatectomy was used. Correspondences between whole mount specimens and MRI and MRF were manually established. Prostatitis, PCa, and normal peripheral zone (PZ) regions of interest (ROIs) on pathology were segmented for TCRs of epithelium, lumen, and stroma using two U-net deep learning models. Corresponding ROIs were mapped to T2-weighted MRI (T2w), apparent diffusion coefficient (ADC), and T1 and T2 MRF maps. Their correlations with TCRs were computed using Pearson's correlation coefficient (R). Statistically significant differences in means were assessed using one-way ANOVA.

RESULTS

Statistically significant differences (p < 0.01) in means of TCRs and T1 and T2 MRF were observed between PCa, prostatitis, and normal PZ. A negative correlation was observed between T1 and T2 MRF and epithelium (R = - 0.38, - 0.44, p < 0.05) of PCa. T1 MRF was correlated in opposite directions with stroma of PCa and prostatitis (R = 0.35, - 0.44, p < 0.05). T2 MRF was positively correlated with lumen of PCa and prostatitis (R = 0.57, 0.46, p < 0.01). Mean T2 MRF showed significant differences (p < 0.01) between PCa and prostatitis across both transition zone (TZ) and PZ, while mean T1 MRF was significant (p = 0.02) in TZ.

CONCLUSION

Significant associations between MRF (T1 in the TZ and T2 in the PZ) and tissue compartments on corresponding histopathology were observed.

KEY POINTS

• Mean T2 MRF measurements and ADC within cancerous regions of interest dropped with increasing ISUP prognostic groups (IPG). • Mean T1 and T2 MRF measurements were significantly different (p < 0.001) across IPGs, prostatitis, and normal peripheral zone (NPZ). • T2 MRF showed stronger correlations in the peripheral zone, while T1 MRF showed stronger correlations in the transition zone with histopathology for prostate cancer.

Registration of presurgical MRI and histopathology images from radical prostatectomy via RAPSODI

PURPOSE

Magnetic resonance imaging (MRI) has great potential to improve prostate cancer diagnosis; however, subtle differences between cancer and confounding conditions render prostate MRI interpretation challenging. The tissue collected from patients who undergo radical prostatectomy provides a unique opportunity to correlate histopathology images of the prostate with preoperative MRI to accurately map the extent of cancer from histopathology images onto MRI. We seek to develop an open-source, easy-to-use platform to align presurgical MRI and histopathology images of resected prostates in patients who underwent radical prostatectomy to create accurate cancer labels on MRI.

METHODS

Here, we introduce RAdiology Pathology Spatial Open-Source multi-Dimensional Integration (RAPSODI), the first open-source framework for the registration of radiology and pathology images. RAPSODI relies on three steps. First, it creates a three-dimensional (3D) reconstruction of the histopathology specimen as a digital representation of the tissue before gross sectioning. Second, RAPSODI registers corresponding histopathology and MRI slices. Third, the optimized transforms are applied to the cancer regions outlined on the histopathology images to project those labels onto the preoperative MRI.

RESULTS

We tested RAPSODI in a phantom study where we simulated various conditions, for example, tissue shrinkage during fixation. Our experiments showed that RAPSODI can reliably correct multiple artifacts. We also evaluated RAPSODI in 157 patients from three institutions that underwent radical prostatectomy and have very different pathology processing and scanning. RAPSODI was evaluated in 907 corresponding histpathology-MRI slices and achieved a Dice coefficient of 0.97 ± 0.01 for the prostate, a Hausdorff distance of 1.99 ± 0.70 mm for the prostate boundary, a urethra deviation of 3.09 ± 1.45 mm, and a landmark deviation of 2.80 ± 0.59 mm between registered histopathology images and MRI.

CONCLUSION

Our robust framework successfully mapped the extent of cancer from histopathology slices onto MRI providing labels from training machine learning methods to detect cancer on MRI.

Automated Classification of Significant Prostate Cancer on MRI: A Systematic Review on the Performance of Machine Learning Applications

Significant prostate carcinoma (sPCa) classification based on MRI using radiomics or deep learning approaches has gained much interest, due to the potential application in assisting in clinical decision-making.

OBJECTIVE

To systematically review the literature (i) to determine which algorithms are most frequently used for sPCa classification, (ii) to investigate whether there exists a relation between the performance and the method or the MRI sequences used, (iii) to assess what study design factors affect the performance on sPCa classification, and (iv) to research whether performance had been evaluated in a clinical setting Methods: The databases Embase and Ovid MEDLINE were searched for studies describing machine learning or deep learning classification methods discriminating between significant and nonsignificant PCa on multiparametric MRI that performed a valid validation procedure. Quality was assessed by the modified radiomics quality score. We computed the median area under the receiver operating curve (AUC) from overall methods and the interquartile range.

RESULTS

From 2846 potentially relevant publications, 27 were included. The most frequent algorithms used in the literature for PCa classification are logistic regression (22%) and convolutional neural networks (CNNs) (22%). The median AUC was 0.79 (interquartile range: 0.77-0.87). No significant effect of number of included patients, image sequences, or reference standard on the reported performance was found. Three studies described an external validation and none of the papers described a validation in a prospective clinical trial.

CONCLUSIONS

To unlock the promising potential of machine and deep learning approaches, validation studies and clinical prospective studies should be performed with an established protocol to assess the added value in decision-making.

Prostate MRI radiomics: A systematic review and radiomic quality score assessment

BACKGROUND

Radiomics have the potential to further increase the value of MRI in prostate cancer management. However, implementation in clinical practice is still far and concerns have been raised regarding the methodological quality of radiomic studies. Therefore, we aimed to systematically review the literature to assess the quality of prostate MRI radiomic studies using the radiomics quality score (RQS).

METHODS

Multiple medical literature archives (PubMed, Web of Science and EMBASE) were searched to retrieve original investigations focused on prostate MRI radiomic approaches up to the end of June 2019. Three researchers independently assessed each paper using the RQS. Data from the most experienced researcher were used for descriptive analysis. Inter-rater reproducibility was assessed using the intraclass correlation coefficient (ICC) on the total RQS score.

RESULTS

73 studies were included in the analysis. Overall, the average RQS total score was 7.93 ± 5.13 on a maximum of 36 points, with a final average percentage of 23 ± 13%. Among the most critical items, the lack of feature robustness testing strategies and external validation datasets. The ICC resulted poor to moderate, with an average value of 0.57 and 95% Confidence Intervals between 0.44 and 0.69.

CONCLUSIONS

Current studies on prostate MRI radiomics still lack the quality required to allow their introduction in clinical practice.

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

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.

Use of Precision Imaging in the Evaluation of Pancreas Cancer

Pancreas cancer is an aggressive and fatal disease that will become one of the leading causes of cancer mortality by 2030. An all-out effort is underway to better understand the basic biologic mechanisms of this disease ranging from early development to metastatic disease. In order to change the course of this disease, diagnostic radiology imaging may play a vital role in providing a precise, noninvasive method for early diagnosis and assessment of treatment response. Recent progress in combining medical imaging, advanced image analysis and artificial intelligence, termed radiomics, can offer an innovate approach in detecting the earliest changes of tumor development as well as a rapid method for the detection of response. In this chapter, we introduce the principles of radiomics and demonstrate how it can provide additional information into tumor biology, early detection, and response assessments advancing the goals of precision imaging to deliver the right treatment to the right person at the right time.

CT-based radiomics features analysis for predicting the risk of anterior mediastinal lesions

Background

To retrospectively validate CT-based radiomics features for predicting the risk of anterior mediastinal lesions.

Methods

A retrospective study was performed through February 2013 to March 2018 on 298 patients who had pathologically confirmed anterior mediastinal lesions. The patients all underwent CT scans before their treatment, including 130 unenhanced computed tomography (UECT) and 168 contrast-enhanced CT (CECT) scans. The lesion areas were delineated, and a total of 1,029 radiomics features were extracted. The least absolute shrinkage and selection operator (Lasso) algorithm method was used to select the radiomics features significantly associated with discrimination of high-risk from low-risk lesions in the anterior mediastinum. Then, 8-fold and 3-fold cross-validation logistic regression (LR) models were taken as the feature selection classifiers to build the radiomics models for UECT and CECT scan respectively. The predictive performance of the radiomics features was evaluated based on the receiver operating characteristics (ROC) curve.

Results

Each of the two radiomics classifiers included the optimal 12 radiomic features. In terms of the area under ROC curve, using the radiomics model in discriminating high-risk lesions from the low-risks, CECT images accounted for 74.1% with a sensitivity of 66.67% and specificity of 64.81%. Meanwhile, UECT images were 84.2% with a sensitivity of 71.43% and specificity of 74.07%.

Conclusions

The association of the two proposed CT-based radiomics features with the discrimination of high and low-risk lesions in anterior mediastinum was confirmed, and the radiomics features of the UECT scan were proven to have better prediction performance than the CECT's in risk grading.