Radiomics in radiooncology - Challenging the medical physicist

Tumor grading of soft tissue sarcomas using MRI-based radiomics

Background

Treatment decisions for multimodal therapy in soft tissue sarcoma (STS) patients greatly depend on the differentiation between low-grade and high-grade tumors. We developed MRI-based radiomics grading models for the differentiation between low-grade (G1) and high-grade (G2/G3) STS.

Methods

The study was registered at ClinicalTrials.gov (number NCT03798795). Contrast-enhanced T1-weighted fat saturated (T1FSGd), fat-saturated T2-weighted (T2FS) MRI sequences, and tumor grading following the French Federation of Cancer Centers Sarcoma Group obtained from pre-therapeutic biopsies were gathered from two independent retrospective patient cohorts. Volumes of interest were manually segmented. After preprocessing, 1394 radiomics features were extracted from each sequence. Features unstable in 21 independent multiple-segmentations were excluded. Least absolute shrinkage and selection operator models were developed using nested cross-validation on a training patient cohort (122 patients). The influence of ComBatHarmonization was assessed for correction of batch effects.

Findings

Three radiomic models based on T2FS, T1FSGd and a combined model achieved predictive performances with an area under the receiver operator characteristic curve (AUC) of 0.78, 0.69, and 0.76 on the independent validation set (103 patients), respectively. The T2FS-based model showed the best reproducibility. The radiomics model involving T1FSGd-based features achieved significant patient stratification. Combining the T2FS radiomic model into a nomogram with clinical staging improved prognostic performance and the clinical net benefit above clinical staging alone.

Interpretation

MRI-based radiomics tumor grading models effectively classify low-grade and high-grade soft tissue sarcomas.

Fund

The authors received support by the medical faculty of the Technical University of Munich and the German Cancer Consortium.

Reliability of tumor segmentation in glioblastoma: Impact on the robustness of MRI-radiomic features

PURPOSE

The use of radiomic features as biomarkers of treatment response and outcome or as correlates to genomic variations requires that the computed features are robust and reproducible. Segmentation, a crucial step in radiomic analysis, is a major source of variability in the computed radiomic features. Therefore, we studied the impact of tumor segmentation variability on the robustness of MRI radiomic features.

METHOD

Fluid-attenuated inversion recovery (FLAIR) and contrast-enhanced T1-weighted (T1WI_CE ) MRI of 90 patients diagnosed with glioblastoma were segmented using a semiautomatic algorithm and an interactive segmentation with two different raters. We analyzed the robustness of 108 radiomic features from five categories (intensity histogram, gray-level co-occurrence matrix, gray-level size-zone matrix (GLSZM), edge maps, and shape) using intra-class correlation coefficient (ICC) and Bland and Altman analysis.

RESULTS

Our results show that both segmentation methods are reliable with ICC ≥ 0.96 and standard deviation (SD) of mean differences between the two raters (SD_diffs ) ≤ 30%. Features computed from the histogram and co-occurrence matrices were found to be the most robust (ICC ≥ 0.8 and SD_diffs  ≤ 30% for most features in these groups). Features from GLSZM were shown to have mixed robustness. Edge, shape, and GLSZM features were the most impacted by the choice of segmentation method with the interactive method resulting in more robust features than the semiautomatic method. Finally, features computed from T1WI_CE and FLAIR images were found to have similar robustness when computed with the interactive segmentation method.

CONCLUSION

Semiautomatic and interactive segmentation methods using two raters are both reliable. The interactive method produced more robust features than the semiautomatic method. We also found that the robustness of radiomic features varied by categories. Therefore, this study could help motivate segmentation methods and feature selection in MRI radiomic studies.

Radiogenomics: bridging imaging and genomics

From diagnostics to prognosis to response prediction, new applications for radiomics are rapidly being developed. One of the fastest evolving branches involves linking imaging phenotypes to the tumor genetic profile, a field commonly referred to as "radiogenomics." In this review, a general outline of radiogenomic literature concerning prominent mutations across different tumor sites will be provided. The field of radiogenomics originates from image processing techniques developed decades ago; however, many technical and clinical challenges still need to be addressed. Nevertheless, increasingly accurate and robust radiogenomic models are being presented and the future appears to be bright.

An overview of deep learning in medical imaging focusing on MRI

What has happened in machine learning lately, and what does it mean for the future of medical image analysis? Machine learning has witnessed a tremendous amount of attention over the last few years. The current boom started around 2009 when so-called deep artificial neural networks began outperforming other established models on a number of important benchmarks. Deep neural networks are now the state-of-the-art machine learning models across a variety of areas, from image analysis to natural language processing, and widely deployed in academia and industry. These developments have a huge potential for medical imaging technology, medical data analysis, medical diagnostics and healthcare in general, slowly being realized. We provide a short overview of recent advances and some associated challenges in machine learning applied to medical image processing and image analysis. As this has become a very broad and fast expanding field we will not survey the entire landscape of applications, but put particular focus on deep learning in MRI. Our aim is threefold: (i) give a brief introduction to deep learning with pointers to core references; (ii) indicate how deep learning has been applied to the entire MRI processing chain, from acquisition to image retrieval, from segmentation to disease prediction; (iii) provide a starting point for people interested in experimenting and perhaps contributing to the field of deep learning for medical imaging by pointing out good educational resources, state-of-the-art open-source code, and interesting sources of data and problems related medical imaging.

Human Glioma Migration and Infiltration Properties as a Target for Personalized Radiation Medicine

Gliomas are primary brain tumors that present the majority of malignant adult brain tumors. Gliomas are subdivided into low- and high-grade tumors. Despite extensive research in recent years, the prognosis of malignant glioma patients remains poor. This is caused by naturally highly infiltrative capacities as well as high levels of radio- and chemoresistance. Additionally, it was shown that low linear energy transfer (LET) irradiation enhances migration and invasion of several glioma entities which might counteract today’s treatment concepts. However, this finding is discussed controversially. In the era of personalized medicine, this controversial data might be attributed to the patient-specific heterogeneity that ultimately could be used for treatment. Thus, current developments in glioma therapy should be seen in the context of intrinsic and radiation-enhanced migration and invasion. Due to the natural heterogeneity of glioma cells and different radiation responses, a personalized radiation treatment concept is suggested and alternative radiation concepts are discussed.

The European Federation of Organisations for Medical Physics (EFOMP) White Paper: Big data and deep learning in medical imaging and in relation to medical physics profession

Big data and deep learning will profoundly change various areas of professions and research in the future. This will also happen in medicine and medical imaging in particular. As medical physicists, we should pursue beyond the concept of technical quality to extend our methodology and competence towards measuring and optimising the diagnostic value in terms of how it is connected to care outcome. Functional implementation of such methodology requires data processing utilities starting from data collection and management and culminating in the data analysis methods. Data quality control and validation are prerequisites for the deep learning application in order to provide reliable further analysis, classification, interpretation, probabilistic and predictive modelling from the vast heterogeneous big data. Challenges in practical data analytics relate to both horizontal and longitudinal analysis aspects. Quantitative aspects of data validation, quality control, physically meaningful measures, parameter connections and system modelling for the future artificial intelligence (AI) methods are positioned firmly in the field of Medical Physics profession. It is our interest to ensure that our professional education, continuous training and competence will follow this significant global development.

Radiomics: the facts and the challenges of image analysis

Radiomics is an emerging translational field of research aiming to extract mineable high-dimensional data from clinical images. The radiomic process can be divided into distinct steps with definable inputs and outputs, such as image acquisition and reconstruction, image segmentation, features extraction and qualification, analysis, and model building. Each step needs careful evaluation for the construction of robust and reliable models to be transferred into clinical practice for the purposes of prognosis, non-invasive disease tracking, and evaluation of disease response to treatment. After the definition of texture parameters (shape features; first-, second-, and higher-order features), we briefly discuss the origin of the term radiomics and the methods for selecting the parameters useful for a radiomic approach, including cluster analysis, principal component analysis, random forest, neural network, linear/logistic regression, and other. Reproducibility and clinical value of parameters should be firstly tested with internal cross-validation and then validated on independent external cohorts. This article summarises the major issues regarding this multi-step process, focussing in particular on challenges of the extraction of radiomic features from data sets provided by computed tomography, positron emission tomography, and magnetic resonance imaging.

Radiomics: the facts and the challenges of image analysis

Radiomics is an emerging translational field of research aiming to extract mineable high-dimensional data from clinical images. The radiomic process can be divided into distinct steps with definable inputs and outputs, such as image acquisition and reconstruction, image segmentation, features extraction and qualification, analysis, and model building. Each step needs careful evaluation for the construction of robust and reliable models to be transferred into clinical practice for the purposes of prognosis, non-invasive disease tracking, and evaluation of disease response to treatment. After the definition of texture parameters (shape features; first-, second-, and higher-order features), we briefly discuss the origin of the term radiomics and the methods for selecting the parameters useful for a radiomic approach, including cluster analysis, principal component analysis, random forest, neural network, linear/logistic regression, and other. Reproducibility and clinical value of parameters should be firstly tested with internal cross-validation and then validated on independent external cohorts. This article summarises the major issues regarding this multi-step process, focussing in particular on challenges of the extraction of radiomic features from data sets provided by computed tomography, positron emission tomography, and magnetic resonance imaging.

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

Computer-aided diagnosis (CAD) is a field that is essentially based on pattern recognition that improves the accuracy of a diagnosis made by a physician who takes into account the computer's "opinion" derived from the quantitative analysis of radiological images. Radiomics is a field based on data science that massively and comprehensively analyzes a large number of medical images to extract a large number of phenotypic features reflecting disease traits, and explores the associations between the features and patients' prognoses for precision medicine. According to the definitions for both, you may think that radiomics is not a paraphrase of CAD, but you may also think that these definitions are "image manipulation". However, there are common and different features between the two fields. This review paper elaborates on these common and different features and introduces the potential of radiomics for cancer diagnosis and treatment by comparing it with CAD.

A computer-aided diagnosis scheme of breast lesion classification using GLGLM and shape features: Combined-view and multi-classifiers

PURPOSE

To address high false-positive results of FFDM issue, we make the first effort to develop a computer-aided diagnosis (CAD) scheme to analyze and distinguish breast lesions.

METHOD

The breast lesion regions were first segmented and depicted on FFDM images from 106 patients. In this work, 11 gray-level gap-length matrix texture features and 12 shape features were extracted form craniocaudal view and mediolateral oblique view, and then Student's t-test, Fisher-score and Relief-F were introduced to select features. We also investigated the effect of three factors, i.e., discretisation, selection methods and classifier methods, of the classification performance via analysis of variance. Finally, a classification model was constructed. Spearman's correlation coefficient analysis was conducted to assess the internal relevance of features.

RESULTS

The proposed scheme using Student's t-test achieved an area under the receiver operating characteristic curve (AUC) value of 0.923 at 512 bins. The AUC values are 0.884, 0.867, 0.874 and 0.901 for the low gray-level gaps emphasis (LGGE), solidity, extent, and the combined set, respectively. Solidity and extent depicts the correlation coefficient of 0.86 (P < 0.05).

CONCLUSIONS

We present a new CAD scheme based on the contribution of the significant factors. The experimental results demonstrate that the presented scheme can be used to successfully distinguish breast carcinoma lesions and benign fibroadenoma lesions in our FFDM dataset and the MIAS dataset, which may provide a CAD method to assist radiologists in diagnosing and interpreting screening mammograms. Moreover, we found that LGGE, solidity and extent features show great potential for breast lesion classification.