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Jensen LJ, Kim D, Elgeti T, Steffen IG, Schaafs LA, Hamm B, Nagel SN. Enhancing the stability of CT radiomics across different volume of interest sizes using parametric feature maps: a phantom study. Eur Radiol Exp 2022; 6:43. [PMID: 36104519 PMCID: PMC9474978 DOI: 10.1186/s41747-022-00297-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In radiomics studies, differences in the volume of interest (VOI) are often inevitable and may confound the extracted features. We aimed to correct this confounding effect of VOI variability by applying parametric maps with a fixed voxel size. METHODS Ten scans of a cup filled with sodium chloride solution were scanned using a multislice computed tomography (CT) unit. Sphere-shaped VOIs with different diameters (4, 8, or 16 mm) were drawn centrally into the phantom. A total of 93 features were extracted conventionally from the original images using PyRadiomics. Using a self-designed and pretested software tool, parametric maps for the same 93 features with a fixed voxel size of 4 mm3 were created. To retrieve the feature values from the maps, VOIs were copied from the original images to preserve the position. Differences in feature quantities between the VOI sizes were tested with the Mann-Whitney U-test and agreement with overall concordance correlation coefficients (OCCC). RESULTS Fifty-five conventionally extracted features were significantly different between the VOI sizes, and none of the features showed excellent agreement in terms of OCCCs. When read from the parametric maps, only 8 features showed significant differences, and 3 features showed an excellent OCCC (≥ 0.85). The OCCCs for 89 features substantially increased using the parametric maps. CONCLUSIONS This phantom study shows that converting CT images into parametric maps resolves the confounding effect of VOI variability and increases feature reproducibility across VOI sizes.
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Affiliation(s)
- Laura J Jensen
- Klinik für Radiologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany.
| | - Damon Kim
- Klinik für Radiologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany.
| | - Thomas Elgeti
- Klinik für Radiologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Ingo G Steffen
- Klinik für Radiologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Lars-Arne Schaafs
- Klinik für Radiologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Bernd Hamm
- Klinik für Radiologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Sebastian N Nagel
- Klinik für Radiologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
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Frood R, Clark M, Burton C, Tsoumpas C, Frangi AF, Gleeson F, Patel C, Scarsbrook A. Utility of pre-treatment FDG PET/CT-derived machine learning models for outcome prediction in classical Hodgkin lymphoma. Eur Radiol 2022; 32:7237-7247. [PMID: 36006428 PMCID: PMC9403224 DOI: 10.1007/s00330-022-09039-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/13/2022] [Accepted: 07/16/2022] [Indexed: 12/22/2022]
Abstract
Objectives Relapse occurs in ~20% of patients with classical Hodgkin lymphoma (cHL) despite treatment adaption based on 2-deoxy-2-[18F]fluoro-d-glucose positron emission tomography/computed tomography response. The objective was to evaluate pre-treatment FDG PET/CT–derived machine learning (ML) models for predicting outcome in patients with cHL. Methods All cHL patients undergoing pre-treatment PET/CT at our institution between 2008 and 2018 were retrospectively identified. A 1.5 × mean liver standardised uptake value (SUV) and a fixed 4.0 SUV threshold were used to segment PET/CT data. Feature extraction was performed using PyRadiomics with ComBat harmonisation. Training (80%) and test (20%) cohorts stratified around 2-year event-free survival (EFS), age, sex, ethnicity and disease stage were defined. Seven ML models were trained and hyperparameters tuned using stratified 5-fold cross-validation. Area under the curve (AUC) from receiver operator characteristic analysis was used to assess performance. Results A total of 289 patients (153 males), median age 36 (range 16–88 years), were included. There was no significant difference between training (n = 231) and test cohorts (n = 58) (p value > 0.05). A ridge regression model using a 1.5 × mean liver SUV segmentation had the highest performance, with mean training, validation and test AUCs of 0.82 ± 0.002, 0.79 ± 0.01 and 0.81 ± 0.12. However, there was no significant difference between a logistic model derived from metabolic tumour volume and clinical features or the highest performing radiomic model. Conclusions Outcome prediction using pre-treatment FDG PET/CT–derived ML models is feasible in cHL patients. Further work is needed to determine optimum predictive thresholds for clinical use. Key points • A fixed threshold segmentation method led to more robust radiomic features. • A radiomic-based model for predicting 2-year event-free survival in classical Hodgkin lymphoma patients is feasible. • A predictive model based on ridge regression was the best performing model on our dataset. Supplementary Information The online version contains supplementary material available at 10.1007/s00330-022-09039-0.
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Affiliation(s)
- Russell Frood
- Department of Nuclear Medicine, Leeds Teaching Hospitals NHS Trust, Leeds, UK. .,Department of Radiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK. .,Leeds Institute of Health Research, University of Leeds, Leeds, UK.
| | - Matt Clark
- Department of Radiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Cathy Burton
- Department of Haematology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Charalampos Tsoumpas
- Department of Nuclear Medicine and Molecular Imaging, University Medical Center of Groningen, University of Groningen, Groningen, Netherlands.,Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Alejandro F Frangi
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK.,Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), School of Computing and School of Medicine, University of Leeds, Leeds, UK.,Medical Imaging Research Center (MIRC), University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium
| | - Fergus Gleeson
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chirag Patel
- Department of Nuclear Medicine, Leeds Teaching Hospitals NHS Trust, Leeds, UK.,Department of Radiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Andrew Scarsbrook
- Department of Nuclear Medicine, Leeds Teaching Hospitals NHS Trust, Leeds, UK.,Department of Radiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK.,Leeds Institute of Health Research, University of Leeds, Leeds, UK
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The potential of predictive and prognostic breast MRI (P2-bMRI). Eur Radiol Exp 2022; 6:42. [PMID: 35989400 PMCID: PMC9393116 DOI: 10.1186/s41747-022-00291-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
Magnetic resonance imaging (MRI) is an important part of breast cancer diagnosis and multimodal workup. It provides unsurpassed soft tissue contrast to analyse the underlying pathophysiology, and it is adopted for a variety of clinical indications. Predictive and prognostic breast MRI (P2-bMRI) is an emerging application next to these indications. The general objective of P2-bMRI is to provide predictive and/or prognostic biomarkers in order to support personalisation of breast cancer treatment. We believe P2-bMRI has a great clinical potential, thanks to the in vivo examination of the whole tumour and of the surrounding tissue, establishing a link between pathophysiology and response to therapy (prediction) as well as patient outcome (prognostication). The tools used for P2-bMRI cover a wide spectrum: standard and advanced multiparametric pulse sequences; structured reporting criteria (for instance BI-RADS descriptors); artificial intelligence methods, including machine learning (with emphasis on radiomics data analysis); and deep learning that have shown compelling potential for this purpose. P2-bMRI reuses the imaging data of examinations performed in the current practice. Accordingly, P2-bMRI could optimise clinical workflow, enabling cost savings and ultimately improving personalisation of treatment. This review introduces the concept of P2-bMRI, focusing on the clinical application of P2-bMRI by using semantic criteria.
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Karabacak M, Ozkara BB, Mordag S, Bisdas S. Deep learning for prediction of isocitrate dehydrogenase mutation in gliomas: a critical approach, systematic review and meta-analysis of the diagnostic test performance using a Bayesian approach. Quant Imaging Med Surg 2022; 12:4033-4046. [PMID: 35919062 PMCID: PMC9338374 DOI: 10.21037/qims-22-34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/25/2022] [Indexed: 11/08/2022]
Abstract
Background Conventionally, identifying isocitrate dehydrogenase (IDH) mutation in gliomas is based on histopathological analysis of tissue specimens acquired via stereotactic biopsy or definitive resection. Accurate pre-treatment prediction of IDH mutation status using magnetic resonance imaging (MRI) can guide clinical decision-making. We aim to evaluate the diagnostic performance of deep learning (DL) to determine IDH mutation status in gliomas. Methods A systematic search of Cochrane Library, Web of Science, Medline, and Scopus was conducted to identify relevant publications until August 1, 2021. Articles were included if all the following criteria were met: (I) patients with histopathologically confirmed World Health Organization (WHO) grade II, III, or IV gliomas; (II) histopathological examination with the IDH mutation; (III) DL was used to predict the IDH mutation status; (IV) sufficient data for reconstruction of confusion matrices in terms of the diagnostic performance of the DL algorithms; and (V) original research articles. Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) and Checklist for Artificial Intelligence in Medical Imaging (CLAIM) was used to assess the studies' quality. Bayes theorem was utilized to calculate the posttest probability. Results Four studies with a total of 1,295 patients were included. In the training set, the pooled sensitivity, specificity, and area under the summary receiver operating characteristic (SROC) curve were 93.9%, 90.9% and 0.958, respectively. In the validation set, the pooled sensitivity, specificity, and area under the SROC curve were 90.8%, 85.5% and 0.939, respectively. With a known pretest probability of 80.2%, the Bayes theorem yielded a posttest probability of 97.6% and 96.0% for a positive test and 27.0% and 30.6% for a negative test for training sets and validation sets, respectively. Discussion This is the first meta-analysis that summarizes the diagnostic performance of DL in predicting IDH mutation status in gliomas via the Bayes theorem. DL algorithms demonstrate excellent diagnostic performance in predicting IDH mutation in gliomas. Radiomic features associated with IDH mutation, and its underlying pathophysiology extracted from advanced MRI may improve prediction probability. However, more studies are required to optimize and increase its reliability. Limitations include obtaining some data via email and lack of training and test sets statistics.
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Affiliation(s)
- Mert Karabacak
- Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Cerrahpasa, Istanbul, Turkey
| | - Burak Berksu Ozkara
- Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Cerrahpasa, Istanbul, Turkey
| | - Seren Mordag
- Faculty of Medicine, Hacettepe University, Sihhiye, Ankara, Turkey
| | - Sotirios Bisdas
- Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, UK
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Lee SY, Ha S, Jeon MG, Li H, Choi H, Kim HP, Choi YR, I H, Jeong YJ, Park YH, Ahn H, Hong SH, Koo HJ, Lee CW, Kim MJ, Kim YJ, Kim KW, Choi JM. Localization-adjusted diagnostic performance and assistance effect of a computer-aided detection system for pneumothorax and consolidation. NPJ Digit Med 2022; 5:107. [PMID: 35908091 PMCID: PMC9339006 DOI: 10.1038/s41746-022-00658-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022] Open
Abstract
While many deep-learning-based computer-aided detection systems (CAD) have been developed and commercialized for abnormality detection in chest radiographs (CXR), their ability to localize a target abnormality is rarely reported. Localization accuracy is important in terms of model interpretability, which is crucial in clinical settings. Moreover, diagnostic performances are likely to vary depending on thresholds which define an accurate localization. In a multi-center, stand-alone clinical trial using temporal and external validation datasets of 1,050 CXRs, we evaluated localization accuracy, localization-adjusted discrimination, and calibration of a commercially available deep-learning-based CAD for detecting consolidation and pneumothorax. The CAD achieved image-level AUROC (95% CI) of 0.960 (0.945, 0.975), sensitivity of 0.933 (0.899, 0.959), specificity of 0.948 (0.930, 0.963), dice of 0.691 (0.664, 0.718), moderate calibration for consolidation, and image-level AUROC of 0.978 (0.965, 0.991), sensitivity of 0.956 (0.923, 0.978), specificity of 0.996 (0.989, 0.999), dice of 0.798 (0.770, 0.826), moderate calibration for pneumothorax. Diagnostic performances varied substantially when localization accuracy was accounted for but remained high at the minimum threshold of clinical relevance. In a separate trial for diagnostic impact using 461 CXRs, the causal effect of the CAD assistance on clinicians' diagnostic performances was estimated. After adjusting for age, sex, dataset, and abnormality type, the CAD improved clinicians' diagnostic performances on average (OR [95% CI] = 1.73 [1.30, 2.32]; p < 0.001), although the effects varied substantially by clinical backgrounds. The CAD was found to have high stand-alone diagnostic performances and may beneficially impact clinicians' diagnostic performances when used in clinical settings.
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Affiliation(s)
- Sun Yeop Lee
- Department of Medical Artificial Intelligence, Deepnoid, Inc., Seoul, Republic of Korea
| | - Sangwoo Ha
- Department of Medical Artificial Intelligence, Deepnoid, Inc., Seoul, Republic of Korea
| | - Min Gyeong Jeon
- Department of Medical Artificial Intelligence, Deepnoid, Inc., Seoul, Republic of Korea
| | - Hao Li
- Department of Medical Artificial Intelligence, Deepnoid, Inc., Seoul, Republic of Korea
| | - Hyunju Choi
- Department of Medical Artificial Intelligence, Deepnoid, Inc., Seoul, Republic of Korea
| | - Hwa Pyung Kim
- Department of Medical Artificial Intelligence, Deepnoid, Inc., Seoul, Republic of Korea
| | - Ye Ra Choi
- Department of Radiology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Republic of Korea
- Department of Radiology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hoseok I
- Department of Thoracic and Cardiovascular Surgery, Pusan National University School of Medicine, Busan, Republic of Korea
- Convergence Medical Institute of Technology, Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Yeon Joo Jeong
- Department of Radiology and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Yoon Ha Park
- Department of Internal Medicine, Jawol Health Center, Incheon, Republic of Korea
| | - Hyemin Ahn
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang Hyup Hong
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hyun Jung Koo
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Choong Wook Lee
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Min Jae Kim
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yeon Joo Kim
- Department of Respiratory Allergy Medicine, Nowon Eulji Medical Center, Seoul, Republic of Korea
| | - Kyung Won Kim
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jong Mun Choi
- Department of Medical Artificial Intelligence, Deepnoid, Inc., Seoul, Republic of Korea.
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Woznicki P, Laqua F, Bley T, Baeßler B. AutoRadiomics: A Framework for Reproducible Radiomics Research. FRONTIERS IN RADIOLOGY 2022; 2:919133. [PMID: 37492662 PMCID: PMC10365084 DOI: 10.3389/fradi.2022.919133] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/20/2022] [Indexed: 07/27/2023]
Abstract
Purpose Machine learning based on radiomics features has seen huge success in a variety of clinical applications. However, the need for standardization and reproducibility has been increasingly recognized as a necessary step for future clinical translation. We developed a novel, intuitive open-source framework to facilitate all data analysis steps of a radiomics workflow in an easy and reproducible manner and evaluated it by reproducing classification results in eight available open-source datasets from different clinical entities. Methods The framework performs image preprocessing, feature extraction, feature selection, modeling, and model evaluation, and can automatically choose the optimal parameters for a given task. All analysis steps can be reproduced with a web application, which offers an interactive user interface and does not require programming skills. We evaluated our method in seven different clinical applications using eight public datasets: six datasets from the recently published WORC database, and two prostate MRI datasets-Prostate MRI and Ultrasound With Pathology and Coordinates of Tracked Biopsy (Prostate-UCLA) and PROSTATEx. Results In the analyzed datasets, AutoRadiomics successfully created and optimized models using radiomics features. For WORC datasets, we achieved AUCs ranging from 0.56 for lung melanoma metastases detection to 0.93 for liposarcoma detection and thereby managed to replicate the previously reported results. No significant overfitting between training and test sets was observed. For the prostate cancer detection task, results were better in the PROSTATEx dataset (AUC = 0.73 for prostate and 0.72 for lesion mask) than in the Prostate-UCLA dataset (AUC 0.61 for prostate and 0.65 for lesion mask), with external validation results varying from AUC = 0.51 to AUC = 0.77. Conclusion AutoRadiomics is a robust tool for radiomic studies, which can be used as a comprehensive solution, one of the analysis steps, or an exploratory tool. Its wide applicability was confirmed by the results obtained in the diverse analyzed datasets. The framework, as well as code for this analysis, are publicly available under https://github.com/pwoznicki/AutoRadiomics.
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Meningioma Radiomics: At the Nexus of Imaging, Pathology and Biomolecular Characterization. Cancers (Basel) 2022; 14:cancers14112605. [PMID: 35681585 PMCID: PMC9179263 DOI: 10.3390/cancers14112605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Meningiomas are typically benign, common extra-axial tumors of the central nervous system. Routine clinical assessment by radiologists presents some limitations regarding long-term patient outcome prediction and risk stratification. Given the exponential growth of interest in radiomics and artificial intelligence in medical imaging, numerous studies have evaluated the potential of these tools in the setting of meningioma imaging. These were aimed at the development of reliable and reproducible models based on quantitative data. Although several limitations have yet to be overcome for their routine use in clinical practice, their innovative potential is evident. In this review, we present a wide-ranging overview of radiomics and artificial intelligence applications in meningioma imaging. Abstract Meningiomas are the most common extra-axial tumors of the central nervous system (CNS). Even though recurrence is uncommon after surgery and most meningiomas are benign, an aggressive behavior may still be exhibited in some cases. Although the diagnosis can be made by radiologists, typically with magnetic resonance imaging, qualitative analysis has some limitations in regard to outcome prediction and risk stratification. The acquisition of this information could help the referring clinician in the decision-making process and selection of the appropriate treatment. Following the increased attention and potential of radiomics and artificial intelligence in the healthcare domain, including oncological imaging, researchers have investigated their use over the years to overcome the current limitations of imaging. The aim of these new tools is the replacement of subjective and, therefore, potentially variable medical image analysis by more objective quantitative data, using computational algorithms. Although radiomics has not yet fully entered clinical practice, its potential for the detection, diagnostic, and prognostic characterization of tumors is evident. In this review, we present a wide-ranging overview of radiomics and artificial intelligence applications in meningioma imaging.
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A Semi-Unsupervised Segmentation Methodology Based on Texture Recognition for Radiomics: A Preliminary Study on Brain Tumours. ELECTRONICS 2022. [DOI: 10.3390/electronics11101573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Because of the intrinsic anatomic complexity of the brain structures, brain tumors have a high mortality and disability rate, and an early diagnosis is mandatory to contain damages. The commonly used biopsy is the diagnostic gold standard method, but it is invasive and, due to intratumoral heterogeneity, biopsies may lead to an incorrect result. Moreover, some tumors cannot be resectable if located in critical eloquent areas. On the other hand, medical imaging procedures can evaluate the entire tumor in a non-invasive and reproducible way. Radiomics is an emerging diagnosis technique based on quantitative medical image analyses, which makes use of data provided by non-invasive diagnosis techniques such as X-ray, computer-tomography (CT), magnetic resonance (MR), and proton emission tomography (PET). Radiomics techniques require the comprehensive analysis of huge numbers of medical images to extract a large and useful number of phenotypic features (usually called radiomics biomarkers). The goal is to explore and obtain the associations between features of tumors, diagnosis and patients’ prognoses to choose the best treatments and maximize the patient’s survival rate. Current radiomics techniques are not standardized in term of segmentation, feature extraction, and selection, moreover, the decision on suitable therapies still requires the supervision of an expert doctor. In this paper, we propose a semi-automatic methodology aimed to help the identification and segmentation of malignant tissues by using the combination of binary texture recognition, growing area algorithm, and machine learning techniques. In particular, the proposed method not only helps to better identify pathologic tissues but also permits to analyze in a fast way the huge amount of data, in Dicom format, provided by non-invasive diagnostic techniques. A preliminary experimental assessment has been conducted, considering a real MRI database of brain tumors. The method has been compared with the segmentation software’s tools “slicer 3D”. The obtained results are quite promising and demonstrate the potentialities of the proposed semi-unsupervised segmentation methodology.
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Borgheresi A, De Muzio F, Agostini A, Ottaviani L, Bruno A, Granata V, Fusco R, Danti G, Flammia F, Grassi R, Grassi F, Bruno F, Palumbo P, Barile A, Miele V, Giovagnoni A. Lymph Nodes Evaluation in Rectal Cancer: Where Do We Stand and Future Perspective. J Clin Med 2022; 11:2599. [PMID: 35566723 PMCID: PMC9104021 DOI: 10.3390/jcm11092599] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022] Open
Abstract
The assessment of nodal involvement in patients with rectal cancer (RC) is fundamental in disease management. Magnetic Resonance Imaging (MRI) is routinely used for local and nodal staging of RC by using morphological criteria. The actual dimensional and morphological criteria for nodal assessment present several limitations in terms of sensitivity and specificity. For these reasons, several different techniques, such as Diffusion Weighted Imaging (DWI), Intravoxel Incoherent Motion (IVIM), Diffusion Kurtosis Imaging (DKI), and Dynamic Contrast Enhancement (DCE) in MRI have been introduced but still not fully validated. Positron Emission Tomography (PET)/CT plays a pivotal role in the assessment of LNs; more recently PET/MRI has been introduced. The advantages and limitations of these imaging modalities will be provided in this narrative review. The second part of the review includes experimental techniques, such as iron-oxide particles (SPIO), and dual-energy CT (DECT). Radiomics analysis is an active field of research, and the evidence about LNs in RC will be discussed. The review also discusses the different recommendations between the European and North American guidelines for the evaluation of LNs in RC, from anatomical considerations to structured reporting.
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Affiliation(s)
- Alessandra Borgheresi
- Department of Clinical, Special and Dental Sciences, University Politecnica delle Marche, 60121 Ancona, Italy; (A.B.); (A.A.); (A.B.); (A.G.)
| | - Federica De Muzio
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Andrea Agostini
- Department of Clinical, Special and Dental Sciences, University Politecnica delle Marche, 60121 Ancona, Italy; (A.B.); (A.A.); (A.B.); (A.G.)
- Department of Radiological Sciences, University Hospital Ospedali Riuniti, 60126 Ancona, Italy;
- Italian Society of Medical and Interventional Radiology (SIRM), SIRM Foundation, 20122 Milan, Italy; (G.D.); (R.G.); (F.G.); (F.B.); (P.P.); (V.M.)
| | - Letizia Ottaviani
- Department of Radiological Sciences, University Hospital Ospedali Riuniti, 60126 Ancona, Italy;
| | - Alessandra Bruno
- Department of Clinical, Special and Dental Sciences, University Politecnica delle Marche, 60121 Ancona, Italy; (A.B.); (A.A.); (A.B.); (A.G.)
| | - Vincenza Granata
- Division of Radiology, Istituto Nazionale Tumori IRCCS Fondazione Pascale IRCCS di Napoli, 80131 Naples, Italy;
| | - Roberta Fusco
- Medical Oncology Division, Igea SpA, 80013 Napoli, Italy
| | - Ginevra Danti
- Italian Society of Medical and Interventional Radiology (SIRM), SIRM Foundation, 20122 Milan, Italy; (G.D.); (R.G.); (F.G.); (F.B.); (P.P.); (V.M.)
- Department of Radiology, Azienda Ospedaliero-Universitaria Careggi, Largo Brambilla 3, 50134 Florence, Italy;
| | - Federica Flammia
- Department of Radiology, Azienda Ospedaliero-Universitaria Careggi, Largo Brambilla 3, 50134 Florence, Italy;
| | - Roberta Grassi
- Italian Society of Medical and Interventional Radiology (SIRM), SIRM Foundation, 20122 Milan, Italy; (G.D.); (R.G.); (F.G.); (F.B.); (P.P.); (V.M.)
- Division of Radiology, Università degli Studi della Campania Luigi Vanvitelli, 80128 Naples, Italy
| | - Francesca Grassi
- Italian Society of Medical and Interventional Radiology (SIRM), SIRM Foundation, 20122 Milan, Italy; (G.D.); (R.G.); (F.G.); (F.B.); (P.P.); (V.M.)
- Division of Radiology, Università degli Studi della Campania Luigi Vanvitelli, 80128 Naples, Italy
| | - Federico Bruno
- Italian Society of Medical and Interventional Radiology (SIRM), SIRM Foundation, 20122 Milan, Italy; (G.D.); (R.G.); (F.G.); (F.B.); (P.P.); (V.M.)
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Pierpaolo Palumbo
- Italian Society of Medical and Interventional Radiology (SIRM), SIRM Foundation, 20122 Milan, Italy; (G.D.); (R.G.); (F.G.); (F.B.); (P.P.); (V.M.)
- Abruzzo Health Unit 1, Department of Diagnostic Imaging, Area of Cardiovascular and Interventional Imaging, 67100 L’Aquila, Italy
| | - Antonio Barile
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Vittorio Miele
- Italian Society of Medical and Interventional Radiology (SIRM), SIRM Foundation, 20122 Milan, Italy; (G.D.); (R.G.); (F.G.); (F.B.); (P.P.); (V.M.)
- Department of Radiology, Azienda Ospedaliero-Universitaria Careggi, Largo Brambilla 3, 50134 Florence, Italy;
| | - Andrea Giovagnoni
- Department of Clinical, Special and Dental Sciences, University Politecnica delle Marche, 60121 Ancona, Italy; (A.B.); (A.A.); (A.B.); (A.G.)
- Department of Radiological Sciences, University Hospital Ospedali Riuniti, 60126 Ancona, Italy;
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Duan J, Qiu Q, Zhu J, Shang D, Dou X, Sun T, Yin Y, Meng X. Reproducibility for Hepatocellular Carcinoma CT Radiomic Features: Influence of Delineation Variability Based on 3D-CT, 4D-CT and Multiple-Parameter MR Images. Front Oncol 2022; 12:881931. [PMID: 35494061 PMCID: PMC9047864 DOI: 10.3389/fonc.2022.881931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/21/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Accurate lesion segmentation is a prerequisite for radiomic feature extraction. It helps to reduce the features variability so as to improve the reporting quality of radiomics study. In this research, we aimed to conduct a radiomic feature reproducibility test of inter-/intra-observer delineation variability in hepatocellular carcinoma using 3D-CT images, 4D-CT images and multiple-parameter MR images. Materials and Methods For this retrospective study, 19 HCC patients undergoing 3D-CT, 4D-CT and multiple-parameter MR scans were included in this study. The gross tumor volume (GTV) was independently delineated twice by two observers based on contrast-enhanced computed tomography (CECT), maximum intensity projection (MIP), LAVA-Flex, T2W FRFSE and DWI-EPI images. We also delineated the peritumoral region, which was defined as 0 to 5 mm radius surrounding the GTV. 107 radiomic features were automatically extracted from CECT images using 3D-Slicer software. Quartile coefficient of dispersion (QCD) and intraclass correlation coefficient (ICC) were applied to assess the variability of each radiomic feature. QCD<10% and ICC≥0.75 were considered small variations and excellent reliability. Finally, the principal component analysis (PCA) was used to test the feasibility of dimensionality reduction. Results For tumor tissues, the numbers of radiomic features with QCD<10% indicated no obvious inter-/intra-observer differences or discrepancies in 3D-CT, 4D-CT and multiple-parameter MR delineation. However, the number of radiomic features (mean 89) with ICC≥0.75 was the highest in the multiple-parameter MR group, followed by the 3DCT group (mean 77) and the MIP group (mean 73). The peritumor tissues also showed similar results. A total of 15 and 7 radiomic features presented excellent reproducibility and small variation in tumor and peritumoral tissues, respectively. Two robust features showed excellent reproducibility and small variation in tumor and peritumoral tissues. In addition, the values of the two features both represented statistically significant differences among tumor and peritumoral tissues (P<0.05). The PCA results indicated that the first seven principal components could preserve at least 90% of the variance of the original set of features. Conclusion Delineation on multiple-parameter MR images could help to improve the reproducibility of the HCC CT radiomic features and weaken the inter-/intra-observer influence.
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Affiliation(s)
- Jinghao Duan
- School of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, China
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qingtao Qiu
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Jian Zhu
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Dongping Shang
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xue Dou
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Tao Sun
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yong Yin
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xiangjuan Meng
- Department of Clinical Laboratory, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital and Institute, Jinan, China
- *Correspondence: Xiangjuan Meng,
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Fatania K, Clark A, Frood R, Scarsbrook A, Al-Qaisieh B, Currie S, Nix M. Harmonisation of scanner-dependent contrast variations in magnetic resonance imaging for radiation oncology, using style-blind auto-encoders. Phys Imaging Radiat Oncol 2022; 22:115-122. [PMID: 35619643 PMCID: PMC9127401 DOI: 10.1016/j.phro.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022] Open
Abstract
Background and purpose Magnetic Resonance Imaging (MRI) exhibits scanner dependent contrast, which limits generalisability of radiomics and machine-learning for radiation oncology. Current deep-learning harmonisation requires paired data, retraining for new scanners and often suffers from geometry-shift which alters anatomical information. The aim of this study was to investigate style-blind auto-encoders for MRI harmonisation to accommodate unpaired training data, avoid geometry-shift and harmonise data from previously unseen scanners. Materials and methods A style-blind auto-encoder, using adversarial classification on the latent-space, was designed for MRI harmonisation. The public CC359 T1-w MRI brain dataset includes six scanners (three manufacturers, two field strengths), of which five were used for training. MRI from all six (including one unseen) scanner were harmonised to common contrast. Harmonisation extent was quantified via Kolmogorov-Smirnov testing of residual scanner dependence of 3D radiomic features, and compared to WhiteStripe normalisation. Anatomical content preservation was measured through change in structural similarity index on contrast-cycling (δSSIM). Results The percentage of radiomics features showing statistically significant scanner-dependence was reduced from 41% (WhiteStripe) to 16% for white matter and from 39% to 27% for grey matter. δSSIM < 0.0025 on harmonisation and de-harmonisation indicated excellent anatomical content preservation. Conclusions Our method harmonised MRI contrast effectively, preserved critical anatomical details at high fidelity, trained on unpaired data and allowed zero-shot harmonisation. Robust and clinically translatable harmonisation of MRI will enable generalisable radiomic and deep-learning models for a range of applications, including radiation oncology treatment stratification, planning and response monitoring.
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Affiliation(s)
- Kavi Fatania
- Department of Radiology, St James University Hospital Trust, Beckett Street, Leeds LS9 7TF, UK
| | - Anna Clark
- Leeds Cancer Centre, Bexley Wing, St James University Hospital Trust, Beckett Street, Leeds LS9 7TF, UK
| | - Russell Frood
- Department of Radiology, St James University Hospital Trust, Beckett Street, Leeds LS9 7TF, UK
| | - Andrew Scarsbrook
- Department of Radiology, St James University Hospital Trust, Beckett Street, Leeds LS9 7TF, UK
| | - Bashar Al-Qaisieh
- Leeds Cancer Centre, Bexley Wing, St James University Hospital Trust, Beckett Street, Leeds LS9 7TF, UK
| | - Stuart Currie
- Department of Radiology, St James University Hospital Trust, Beckett Street, Leeds LS9 7TF, UK
| | - Michael Nix
- Leeds Cancer Centre, Bexley Wing, St James University Hospital Trust, Beckett Street, Leeds LS9 7TF, UK
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Discovery of Pre-Treatment FDG PET/CT-Derived Radiomics-Based Models for Predicting Outcome in Diffuse Large B-Cell Lymphoma. Cancers (Basel) 2022; 14:cancers14071711. [PMID: 35406482 PMCID: PMC8997127 DOI: 10.3390/cancers14071711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Diffuse large B-cell lymphoma (DLBCL) is the most common type of lymphoma. Even with the improvements in the treatment of DLBCL, around a quarter of patients will experience recurrence. The aim of this single centre retrospective study was to predict which patients would have recurrence within 2 years of their treatment using machine learning techniques based on radiomics extracted from the staging PET/CT images. Our study demonstrated that in our dataset of 229 patients (training data = 183, test data = 46) that a combined radiomic and clinical based model performed better than a simple model based on metabolic tumour volume, and that it had a good predictive ability which was maintained when tested on an unseen test set. Abstract Background: Approximately 30% of patients with diffuse large B-cell lymphoma (DLBCL) will have recurrence. The aim of this study was to develop a radiomic based model derived from baseline PET/CT to predict 2-year event free survival (2-EFS). Methods: Patients with DLBCL treated with R-CHOP chemotherapy undergoing pre-treatment PET/CT between January 2008 and January 2018 were included. The dataset was split into training and internal unseen test sets (ratio 80:20). A logistic regression model using metabolic tumour volume (MTV) and six different machine learning classifiers created from clinical and radiomic features derived from the baseline PET/CT were trained and tuned using four-fold cross validation. The model with the highest mean validation receiver operator characteristic (ROC) curve area under the curve (AUC) was tested on the unseen test set. Results: 229 DLBCL patients met the inclusion criteria with 62 (27%) having 2-EFS events. The training cohort had 183 patients with 46 patients in the unseen test cohort. The model with the highest mean validation AUC combined clinical and radiomic features in a ridge regression model with a mean validation AUC of 0.75 ± 0.06 and a test AUC of 0.73. Conclusions: Radiomics based models demonstrate promise in predicting outcomes in DLBCL patients.
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Rinaldi L, Pezzotta F, Santaniello T, De Marco P, Bianchini L, Origgi D, Cremonesi M, Milani P, Mariani M, Botta F. HeLLePhant: A phantom mimicking non-small cell lung cancer for texture analysis in CT images. Phys Med 2022; 97:13-24. [PMID: 35334407 DOI: 10.1016/j.ejmp.2022.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/01/2022] [Accepted: 03/14/2022] [Indexed: 01/06/2023] Open
Abstract
PURPOSE Phantoms mimicking human tissue heterogeneity and intensity are required to establish radiomic features robustness in Computed Tomography (CT) images. We developed inserts with two different techniques for the radiomic study of Non-Small Cell Lung Cancer (NSCLC) lesions. METHODS We developed two insert prototypes: two 3D-printed made of glycol-modified polyethylene terephthalate (PET-G), and nine with sodium polyacrylate plus iodinated contrast medium. The inserts were put in a handcraft phantom (HeLLePhant). We also analysed four materials of a commercial homogeneous phantom (Catphan® 424) and collected 29 NSCLC patients for comparison. All the CT acquisitions were performed with the same clinical protocol and scanner at 120kVp. The HeLLePhant phantom was scanned ten times in fixed condition at 120kVp and 100kVp for repeatability investigation. We extracted 153 radiomic features using Pyradiomics. To compare the features between phantoms and patients, we computed how many phantom features fell in the range between 10th and 90th percentile of the corresponding patient values. We deemed repeatable the features with a coefficient of variation (CV) less than or equal to 0.10. RESULTS The best similarity with the patients was obtained with the polyacrylate inserts (55.6-90.2%), the worst with Catphan (15.7-19.0%). For the PET-G inserts 35.3% and 36.6% of the features match the patient range. We found high repeatability for all the inserts of the HeLLePhant phantom (74.3-100% at 120kVp, 75.7-97.9% at 100kVp), and observed a texture dependency in repeatability. CONCLUSIONS Our study shows a promising way to construct heterogeneous inserts mimicking a target tissue for radiomic studies.
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Affiliation(s)
- Lisa Rinaldi
- Department of Physics, Università degli Studi di Pavia and INFN, via Bassi 6, 27100 Pavia, Italy; Radiation Research Unit, IEO, European Institute of Oncology IRCCS, via Ripamonti 435, 20141 Milan, Italy.
| | - Federico Pezzotta
- CIMaINa, Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133, Milan, Italy
| | - Tommaso Santaniello
- CIMaINa, Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133, Milan, Italy
| | - Paolo De Marco
- Medical Physics Unit, IEO European Institute of Oncology IRCCS, via Ripamonti 435, 20141 Milan, Italy
| | - Linda Bianchini
- Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133, Milan, Italy
| | - Daniela Origgi
- Medical Physics Unit, IEO European Institute of Oncology IRCCS, via Ripamonti 435, 20141 Milan, Italy
| | - Marta Cremonesi
- Radiation Research Unit, IEO, European Institute of Oncology IRCCS, via Ripamonti 435, 20141 Milan, Italy
| | - Paolo Milani
- CIMaINa, Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133, Milan, Italy
| | - Manuel Mariani
- Department of Physics, Università degli Studi di Pavia and INFN, via Bassi 6, 27100 Pavia, Italy
| | - Francesca Botta
- Medical Physics Unit, IEO European Institute of Oncology IRCCS, via Ripamonti 435, 20141 Milan, Italy
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Radiomics in endometrial cancer and beyond - a perspective from the editors of the EJR. Eur J Radiol 2022; 150:110266. [PMID: 35338953 DOI: 10.1016/j.ejrad.2022.110266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 01/29/2023]
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Waheed W, Saylan S, Hassan T, Kannout H, Alsafar H, Alazzam A. A deep learning-driven low-power, accurate, and portable platform for rapid detection of COVID-19 using reverse-transcription loop-mediated isothermal amplification. Sci Rep 2022; 12:4132. [PMID: 35260715 PMCID: PMC8903312 DOI: 10.1038/s41598-022-07954-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/28/2022] [Indexed: 12/24/2022] Open
Abstract
This paper presents a deep learning-driven portable, accurate, low-cost, and easy-to-use device to perform Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) to facilitate rapid detection of COVID-19. The 3D-printed device-powered using only a 5 Volt AC-DC adapter-can perform 16 simultaneous RT-LAMP reactions and can be used multiple times. Moreover, the experimental protocol is devised to obviate the need for separate, expensive equipment for RNA extraction in addition to eliminating sample evaporation. The entire process from sample preparation to the qualitative assessment of the LAMP amplification takes only 45 min (10 min for pre-heating and 35 min for RT-LAMP reactions). The completion of the amplification reaction yields a fuchsia color for the negative samples and either a yellow or orange color for the positive samples, based on a pH indicator dye. The device is coupled with a novel deep learning system that automatically analyzes the amplification results and pays attention to the pH indicator dye to screen the COVID-19 subjects. The proposed device has been rigorously tested on 250 RT-LAMP clinical samples, where it achieved an overall specificity and sensitivity of 0.9666 and 0.9722, respectively with a recall of 0.9892 for Ct < 30. Also, the proposed system can be widely used as an accurate, sensitive, rapid, and portable tool to detect COVID-19 in settings where access to a lab is difficult, or the results are urgently required.
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Affiliation(s)
- Waqas Waheed
- Department of Mechanical Engineering, Khalifa University, Abu Dhabi, UAE
| | - Sueda Saylan
- System on Chip Center (SOCC), Khalifa University, Abu Dhabi, UAE
- Department of Electrical Engineering and Computer Science, Khalifa University, Abu Dhabi, UAE
| | - Taimur Hassan
- Department of Electrical Engineering and Computer Science, Khalifa University, Abu Dhabi, UAE
- Center for Cyber-Physical Systems (C2PS), EECS Department, Khalifa University, Abu Dhabi, UAE
| | - Hussain Kannout
- Center for Biotechnology (BTC), Khalifa University, Abu Dhabi, UAE
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University, Abu Dhabi, UAE
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Anas Alazzam
- Department of Mechanical Engineering, Khalifa University, Abu Dhabi, UAE.
- System on Chip Center (SOCC), Khalifa University, Abu Dhabi, UAE.
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Tian Y, Komolafe TE, Chen T, Zhou B, Yang X. Prediction of TACE Treatment Response in a Preoperative MRI via Analysis of Integrating Deep Learning and Radiomics Features. J Med Biol Eng 2022. [DOI: 10.1007/s40846-022-00692-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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67
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A novel normalization algorithm to facilitate pre-assessment of Covid-19 disease by improving accuracy of CNN and its FPGA implementation. EVOLVING SYSTEMS 2022. [PMCID: PMC8805671 DOI: 10.1007/s12530-022-09419-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
COVID-19 is still a fatal disease, which has threatened all people by affecting the human lungs. Chest X-Ray or computed tomography imaging is commonly used to make a fast and reliable medical investigation to detect the COVID-19 virus. These medical images are remarkably challenging because it is a full-time job and prone to human errors. In this paper, a new normalization algorithm that consists of Mean–Variance-Softmax-Rescale (MVSR) processes respectively is proposed to provide facilitation pre-assessment and diagnosis Covid-19 disease. In order to show the effect of MVSR normalization technique, the algorithm of proposed method is applied to chest X-ray and Sars-Cov-2 computed tomography images dataset. The normalized X-ray images with MVSR are used to recognize Covid-19 virus via Convolutional Neural Network (CNN) model. At the implementation stage, the MVSR algorithm is executed on MATLAB environment, then all the arithmetic operations of the MVSR normalization are coded in VHDL with the help of fixed-point fractional number representation format on FPGA platform. The experimental platform consists of Zynq-7000 Development FPGA Board and VGA monitor to display the both original and MVSR normalized chest X-ray images. The CNN model is constructed and executed using Anaconda Navigator interface with python language. Based on the results of this study, infections of Covid-19 disease can be easily diagnosed with MVSR normalization technique. The proposed MVSR normalization technique increased the classification accuracy of the CNN model from 83.01, to 96.16% for binary class of chest X-ray images.
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68
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Nasiri H, Alavi SA. A Novel Framework Based on Deep Learning and ANOVA Feature Selection Method for Diagnosis of COVID-19 Cases from Chest X-Ray Images. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:4694567. [PMID: 35013680 PMCID: PMC8742147 DOI: 10.1155/2022/4694567] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
Abstract
Background and Objective. The new coronavirus disease (known as COVID-19) was first identified in Wuhan and quickly spread worldwide, wreaking havoc on the economy and people's everyday lives. As the number of COVID-19 cases is rapidly increasing, a reliable detection technique is needed to identify affected individuals and care for them in the early stages of COVID-19 and reduce the virus's transmission. The most accessible method for COVID-19 identification is Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR); however, it is time-consuming and has false-negative results. These limitations encouraged us to propose a novel framework based on deep learning that can aid radiologists in diagnosing COVID-19 cases from chest X-ray images. Methods. In this paper, a pretrained network, DenseNet169, was employed to extract features from X-ray images. Features were chosen by a feature selection method, i.e., analysis of variance (ANOVA), to reduce computations and time complexity while overcoming the curse of dimensionality to improve accuracy. Finally, selected features were classified by the eXtreme Gradient Boosting (XGBoost). The ChestX-ray8 dataset was employed to train and evaluate the proposed method. Results and Conclusion. The proposed method reached 98.72% accuracy for two-class classification (COVID-19, No-findings) and 92% accuracy for multiclass classification (COVID-19, No-findings, and Pneumonia). The proposed method's precision, recall, and specificity rates on two-class classification were 99.21%, 93.33%, and 100%, respectively. Also, the proposed method achieved 94.07% precision, 88.46% recall, and 100% specificity for multiclass classification. The experimental results show that the proposed framework outperforms other methods and can be helpful for radiologists in the diagnosis of COVID-19 cases.
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Affiliation(s)
- Hamid Nasiri
- Department of Computer Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Seyed Ali Alavi
- Electrical and Computer Engineering Department, Semnan University, Semnan, Iran
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69
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Stability of Liver Radiomics across Different 3D ROI Sizes-An MRI In Vivo Study. Tomography 2021; 7:866-876. [PMID: 34941645 PMCID: PMC8706942 DOI: 10.3390/tomography7040073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/20/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
We aimed to evaluate the stability of radiomic features in the liver of healthy individuals across different three-dimensional regions of interest (3D ROI) sizes in T1-weighted (T1w) and T2-weighted (T2w) images from different MR scanners. We retrospectively included 66 examinations of patients without known diseases or pathological imaging findings acquired on three MRI scanners (3 Tesla I: 25 patients, 3 Tesla II: 19 patients, 1.5 Tesla: 22 patients). 3D ROIs of different diameters (10, 20, 30 mm) were drawn on T1w GRE and T2w TSE images into the liver parenchyma (segment V–VIII). We extracted 93 radiomic features from the different ROIs and tested features for significant differences with the Mann–Whitney-U (MWU)-test. The MWU-test revealed significant differences for most second- and higher-order features, indicating a systematic difference dependent on the ROI size. The features mean, median, root mean squared (RMS), 10th percentile, and 90th percentile were not significantly different. We also assessed feature robustness to ROI size variation with overall concordance correlation coefficients (OCCCs). OCCCs across the different ROI-sizes for mean, median, and RMS were excellent (>0.90) in both sequences on all three scanners. These features, therefore, seem robust to ROI-size variation and suitable for radiomic studies of liver MRI.
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70
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Demircioğlu A. Measuring the bias of incorrect application of feature selection when using cross-validation in radiomics. Insights Imaging 2021; 12:172. [PMID: 34817740 PMCID: PMC8613324 DOI: 10.1186/s13244-021-01115-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/25/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Many studies in radiomics are using feature selection methods to identify the most predictive features. At the same time, they employ cross-validation to estimate the performance of the developed models. However, if the feature selection is performed before the cross-validation, data leakage can occur, and the results can be biased. To measure the extent of this bias, we collected ten publicly available radiomics datasets and conducted two experiments. First, the models were developed by incorrectly applying the feature selection prior to cross-validation. Then, the same experiment was conducted by applying feature selection correctly within cross-validation to each fold. The resulting models were then evaluated against each other in terms of AUC-ROC, AUC-F1, and Accuracy. RESULTS Applying the feature selection incorrectly prior to the cross-validation showed a bias of up to 0.15 in AUC-ROC, 0.29 in AUC-F1, and 0.17 in Accuracy. CONCLUSIONS Incorrect application of feature selection and cross-validation can lead to highly biased results for radiomic datasets.
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Affiliation(s)
- Aydin Demircioğlu
- Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany.
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Xue C, Yuan J, Lo GG, Chang ATY, Poon DMC, Wong OL, Zhou Y, Chu WCW. Radiomics feature reliability assessed by intraclass correlation coefficient: a systematic review. Quant Imaging Med Surg 2021; 11:4431-4460. [PMID: 34603997 DOI: 10.21037/qims-21-86] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
Radiomics research is rapidly growing in recent years, but more concerns on radiomics reliability are also raised. This review attempts to update and overview the current status of radiomics reliability research in the ever expanding medical literature from the perspective of a single reliability metric of intraclass correlation coefficient (ICC). To conduct this systematic review, Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed. After literature search and selection, a total of 481 radiomics studies using CT, PET, or MRI, covering a wide range of subject and disease types, were included for review. In these highly heterogeneous studies, feature reliability to image segmentation was much more investigated than reliability to other factors, such as image acquisition, reconstruction, post-processing, and feature quantification. The reported ICCs also suggested high radiomics feature reliability to image segmentation. Image acquisition was found to introduce much more feature variability than image segmentation, in particular for MRI, based on the reported ICC values. Image post-processing and feature quantification yielded different levels of radiomics reliability and might be used to mitigate image acquisition-induced variability. Some common flaws and pitfalls in ICC use were identified, and suggestions on better ICC use were given. Due to the extremely high study heterogeneities and possible risks of bias, the degree of radiomics feature reliability that has been achieved could not yet be safely synthesized or derived in this review. More future researches on radiomics reliability are warranted.
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Affiliation(s)
- Cindy Xue
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong, China.,Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jing Yuan
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong, China
| | - Gladys G Lo
- Department of Diagnostic & Interventional Radiology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong, China
| | - Amy T Y Chang
- Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong, China
| | - Darren M C Poon
- Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong, China
| | - Oi Lei Wong
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong, China
| | - Yihang Zhou
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong, China
| | - Winnie C W Chu
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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Shur JD, Doran SJ, Kumar S, Ap Dafydd D, Downey K, O'Connor JPB, Papanikolaou N, Messiou C, Koh DM, Orton MR. Radiomics in Oncology: A Practical Guide. Radiographics 2021; 41:1717-1732. [PMID: 34597235 PMCID: PMC8501897 DOI: 10.1148/rg.2021210037] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Radiomics refers to the extraction of mineable data from medical imaging
and has been applied within oncology to improve diagnosis,
prognostication, and clinical decision support, with the goal of
delivering precision medicine. The authors provide a practical approach
for successfully implementing a radiomic workflow from planning and
conceptualization through manuscript writing. Applications in oncology
typically are either classification tasks that involve computing the
probability of a sample belonging to a category, such as benign versus
malignant, or prediction of clinical events with a time-to-event
analysis, such as overall survival. The radiomic workflow is
multidisciplinary, involving radiologists and data and imaging
scientists, and follows a stepwise process involving tumor segmentation,
image preprocessing, feature extraction, model development, and
validation. Images are curated and processed before segmentation, which
can be performed on tumors, tumor subregions, or peritumoral zones.
Extracted features typically describe the distribution of signal
intensities and spatial relationship of pixels within a region of
interest. To improve model performance and reduce overfitting, redundant
and nonreproducible features are removed. Validation is essential to
estimate model performance in new data and can be performed iteratively
on samples of the dataset (cross-validation) or on a separate hold-out
dataset by using internal or external data. A variety of noncommercial
and commercial radiomic software applications can be used. Guidelines
and artificial intelligence checklists are useful when planning and
writing up radiomic studies. Although interest in the field continues to
grow, radiologists should be familiar with potential pitfalls to ensure
that meaningful conclusions can be drawn. Online supplemental material is available for this
article. Published under a CC BY 4.0 license.
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Affiliation(s)
- Joshua D Shur
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
| | - Simon J Doran
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
| | - Santosh Kumar
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
| | - Derfel Ap Dafydd
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
| | - Kate Downey
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
| | - James P B O'Connor
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
| | - Nikolaos Papanikolaou
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
| | - Christina Messiou
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
| | - Dow-Mu Koh
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
| | - Matthew R Orton
- From the Department of Radiology, Royal Marsden Hospital NHS Foundation Trust, Sutton, England (J.D.S., D.a.D., K.D., N. P., C.M., D.M.K.); Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, England (S.J.D., S.K., J.P.B.O., N. P., C.M., D.M.K., M.R.O.); and Computational Clinical Imaging Group, Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal (N.P.)
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Radiomics for Everyone: A New Tool Simplifies Creating Parametric Maps for the Visualization and Quantification of Radiomics Features. Tomography 2021; 7:477-487. [PMID: 34564303 PMCID: PMC8482265 DOI: 10.3390/tomography7030041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/05/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Aim was to develop a user-friendly method for creating parametric maps that would provide a comprehensible visualization and allow immediate quantification of radiomics features. For this, a self-explanatory graphical user interface was designed, and for the proof of concept, maps were created for CT and MR images and features were compared to those from conventional extractions. Especially first-order features were concordant between maps and conventional extractions, some even across all examples. Potential clinical applications were tested on CT and MR images for the differentiation of pulmonary lesions. In these sample applications, maps of Skewness enhanced the differentiation of non-malignant lesions and non-small lung carcinoma manifestations on CT images and maps of Variance enhanced the differentiation of pulmonary lymphoma manifestations and fungal infiltrates on MR images. This new and simple method for creating parametric maps makes radiomics features visually perceivable, allows direct feature quantification by placing a region of interest, can improve the assessment of radiological images and, furthermore, can increase the use of radiomics in clinical routine.
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Fournier L, Costaridou L, Bidaut L, Michoux N, Lecouvet FE, de Geus-Oei LF, Boellaard R, Oprea-Lager DE, Obuchowski NA, Caroli A, Kunz WG, Oei EH, O'Connor JPB, Mayerhoefer ME, Franca M, Alberich-Bayarri A, Deroose CM, Loewe C, Manniesing R, Caramella C, Lopci E, Lassau N, Persson A, Achten R, Rosendahl K, Clement O, Kotter E, Golay X, Smits M, Dewey M, Sullivan DC, van der Lugt A, deSouza NM, European Society Of Radiology. 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. Eur Radiol 2021; 31:6001-6012. [PMID: 33492473 PMCID: PMC8270834 DOI: 10.1007/s00330-020-07598-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
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.
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Affiliation(s)
- Laure Fournier
- PARCC, INSERM, Radiology Department, AP-HP, Hopital europeen Georges Pompidou, Université de Paris, F-75015, Paris, France
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
| | - Lena Costaridou
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- School of Medicine, University of Patras, University Campus, Rio, 26 500, Patras, Greece
| | - Luc Bidaut
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- College of Science, University of Lincoln, Lincoln, LN6 7TS, UK
| | - Nicolas Michoux
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology, Institut de Recherche Expérimentale et Clinique (IREC), Cliniques Universitaires Saint Luc, Université Catholique de Louvain (UCLouvain), B-1200, Brussels, Belgium
| | - Frederic E Lecouvet
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology, Institut de Recherche Expérimentale et Clinique (IREC), Cliniques Universitaires Saint Luc, Université Catholique de Louvain (UCLouvain), B-1200, Brussels, Belgium
| | - Lioe-Fee de Geus-Oei
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Biomedical Photonic Imaging Group, University of Twente, Enschede, The Netherlands
| | - Ronald Boellaard
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology & Nuclear Medicine, Cancer Centre Amsterdam, Amsterdam University Medical Centers (VU University), Amsterdam, The Netherlands
- Quantitative Imaging Biomarkers Alliance, Radiological Society of North America, Oak Brook, IL, USA
| | - Daniela E Oprea-Lager
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology & Nuclear Medicine, Cancer Centre Amsterdam, Amsterdam University Medical Centers (VU University), Amsterdam, The Netherlands
| | - Nancy A Obuchowski
- Quantitative Imaging Biomarkers Alliance, Radiological Society of North America, Oak Brook, IL, USA
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Anna Caroli
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Biomedical Engineering, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Wolfgang G Kunz
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Edwin H Oei
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - James P B O'Connor
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Marius E Mayerhoefer
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Manuela Franca
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology, Centro Hospitalar Universitário do Porto, Instituto de Ciências Biomédicas de Abel Salazar, University of Porto, Porto, Portugal
| | - Angel Alberich-Bayarri
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Quantitative Imaging Biomarkers in Medicine (QUIBIM), Valencia, Spain
| | - Christophe M Deroose
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Nuclear Medicine, University Hospitals Leuven, Leuven, Belgium
- Nuclear Medicine and Molecular Imaging, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Christian Loewe
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Division of Cardiovascular and Interventional Radiology, Dept. for Bioimaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Rashindra Manniesing
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Caroline Caramella
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Radiology Department, Hôpital Marie Lannelongue, Institut d'Oncologie Thoracique, Université Paris-Saclay, Le Plessis-Robinson, France
| | - Egesta Lopci
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Nuclear Medicine, Humanitas Clinical and Research Hospital - IRCCS, Rozzano, MI, Italy
| | - Nathalie Lassau
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Quantitative Imaging Biomarkers Alliance, Radiological Society of North America, Oak Brook, IL, USA
- Imaging Department, Gustave Roussy Cancer Campus Grand, Paris, UMR 1281, INSERM, CNRS, CEA, Universite Paris-Saclay, Saint-Aubin, France
| | - Anders Persson
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology, and Department of Health, Medicine and Caring Sciences, Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Rik Achten
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology and Medical Imaging, Ghent University Hospital, Gent, Belgium
| | - Karen Rosendahl
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology, University Hospital of North Norway, Tromsø, Norway
| | - Olivier Clement
- PARCC, INSERM, Radiology Department, AP-HP, Hopital europeen Georges Pompidou, Université de Paris, F-75015, Paris, France
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
| | - Elmar Kotter
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology, University Medical Center Freiburg, Freiburg, Germany
| | - Xavier Golay
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Quantitative Imaging Biomarkers Alliance, Radiological Society of North America, Oak Brook, IL, USA
- Queen Square Institute of Neurology, University College London, London, UK
| | - Marion Smits
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marc Dewey
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel C Sullivan
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Quantitative Imaging Biomarkers Alliance, Radiological Society of North America, Oak Brook, IL, USA
- Dept. of Radiology, Duke University, 311 Research Dr, Durham, NC, 27710, USA
| | - Aad van der Lugt
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Nandita M deSouza
- European Imaging Biomarkers Alliance (EIBALL), European Society of Radiology, Vienna, Austria.
- Imaging Group, European Organisation of Research and Treatment in Cancer (EORTC), Brussels, Belgium.
- Quantitative Imaging Biomarkers Alliance, Radiological Society of North America, Oak Brook, IL, USA.
- Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK.
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Alshazly H, Linse C, Abdalla M, Barth E, Martinetz T. COVID-Nets: deep CNN architectures for detecting COVID-19 using chest CT scans. PeerJ Comput Sci 2021; 7:e655. [PMID: 34401477 PMCID: PMC8330434 DOI: 10.7717/peerj-cs.655] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/09/2021] [Indexed: 05/10/2023]
Abstract
In this paper we propose two novel deep convolutional network architectures, CovidResNet and CovidDenseNet, to diagnose COVID-19 based on CT images. The models enable transfer learning between different architectures, which might significantly boost the diagnostic performance. Whereas novel architectures usually suffer from the lack of pretrained weights, our proposed models can be partly initialized with larger baseline models like ResNet50 and DenseNet121, which is attractive because of the abundance of public repositories. The architectures are utilized in a first experimental study on the SARS-CoV-2 CT-scan dataset, which contains 4173 CT images for 210 subjects structured in a subject-wise manner into three different classes. The models differentiate between COVID-19, non-COVID-19 viral pneumonia, and healthy samples. We also investigate their performance under three binary classification scenarios where we distinguish COVID-19 from healthy, COVID-19 from non-COVID-19 viral pneumonia, and non-COVID-19 from healthy, respectively. Our proposed models achieve up to 93.87% accuracy, 99.13% precision, 92.49% sensitivity, 97.73% specificity, 95.70% F1-score, and 96.80% AUC score for binary classification, and up to 83.89% accuracy, 80.36% precision, 82.04% sensitivity, 92.07% specificity, 81.05% F1-score, and 94.20% AUC score for the three-class classification tasks. We also validated our models on the COVID19-CT dataset to differentiate COVID-19 and other non-COVID-19 viral infections, and our CovidDenseNet model achieved the best performance with 81.77% accuracy, 79.05% precision, 84.69% sensitivity, 79.05% specificity, 81.77% F1-score, and 87.50% AUC score. The experimental results reveal the effectiveness of the proposed networks in automated COVID-19 detection where they outperform standard models on the considered datasets while being more efficient.
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Affiliation(s)
- Hammam Alshazly
- Institut für Neuro- und Bioinformatik, University of Lübeck, Lübeck, Germany
- Faculty of Computers and Information, South Valley University, Qena, Egypt
| | - Christoph Linse
- Institut für Neuro- und Bioinformatik, University of Lübeck, Lübeck, Germany
| | - Mohamed Abdalla
- Mathematics Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Mathematics Department, Faculty of Science, South Valley University, Qena, Egypt
| | - Erhardt Barth
- Institut für Neuro- und Bioinformatik, University of Lübeck, Lübeck, Germany
| | - Thomas Martinetz
- Institut für Neuro- und Bioinformatik, University of Lübeck, Lübeck, Germany
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Spadarella G, Calareso G, Garanzini E, Ugga L, Cuocolo A, Cuocolo R. MRI based radiomics in nasopharyngeal cancer: Systematic review and perspectives using radiomic quality score (RQS) assessment. Eur J Radiol 2021; 140:109744. [PMID: 33962253 DOI: 10.1016/j.ejrad.2021.109744] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND MRI based radiomics has the potential to better define tumor biology compared to qualitative MRI assessment and support decisions in patients affected by nasopharyngeal carcinoma. Aim of this review was to systematically evaluate the methodological quality of studies using MRI- radiomics for nasopharyngeal cancer patient evaluation. METHODS A systematic search was performed in PUBMED, WEB OF SCIENCE and SCOPUS using "MRI, magnetic resonance imaging, radiomic, texture analysis, nasopharyngeal carcinoma, nasopharyngeal cancer" in all possible combinations. The methodological quality of study included ( = 24) was evaluated according to the RQS (Radiomic quality score). Subgroup, for journal type (imaging/clinical) and biomarker (prognostic/predictive), and correlation, between RQS and journal Impact Factor, analyses were performed. Mann-Whitney U test and Spearman's correlation were performed. P value < .05 were defined as statistically significant. RESULTS Overall, no studies reported a phantom study or a test re-test for assessing stability in image, biological correlation or open science data. Only 8% of them included external validation. Almost half of articles (45 %) performed multivariable analysis with non-radiomics features. Only 1 study was prospective (4%). The mean RQS was 7.5 ± 5.4. No significant differences were detected between articles published in clinical/imaging journal and between studies with a predictive or prognostic biomarker. No significant correlation was found between total RQS and Impact Factor of the year of publication (p always > 0.05). CONCLUSIONS Radiomic articles in nasopharyngeal cancer are mostly of low methodological quality. The greatest limitations are the lack of external validation, biological correlates, prospective design and open science.
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Affiliation(s)
- Gaia Spadarella
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.
| | - Giuseppina Calareso
- Department of Radiology, Fondazione IRCCS, Istituto Nazionale Dei Tumori, Milan, Italy
| | - Enrico Garanzini
- Department of Radiology, Fondazione IRCCS, Istituto Nazionale Dei Tumori, Milan, Italy
| | - Lorenzo Ugga
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Naples, Italy
| | - Alberto Cuocolo
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Naples, Italy
| | - Renato Cuocolo
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, Italy; Laboratory of Augmented Reality for Health Monitoring (ARHeMLab), Department of Electrical Engineering and Information Technology, University of Naples "Federico II", Naples, Italy
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77
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Muenzfeld H, Nowak C, Riedlberger S, Hartenstein A, Hamm B, Jahnke P, Penzkofer T. Intra-scanner repeatability of quantitative imaging features in a 3D printed semi-anthropomorphic CT phantom. Eur J Radiol 2021; 141:109818. [PMID: 34157639 DOI: 10.1016/j.ejrad.2021.109818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Radiomics has shown to provide novel diagnostic and predictive disease information based on quantitative image features in study settings. However, limited data yielded contradictory results and important questions regarding the validity of the methods remain to be answered. The purpose of this study was to evaluate how clinical imaging techniques affect the stability of radiomics features by using 3D printed anthropomorphic CT phantom to test for repeatability and reproducibility of quantitative parameters. METHODS 48 PET/CT validated lymph nodes of prostate cancer patients (24 metastatic, 24 non-metastatic) were used as a template to create a customized 3D printed anthropomorphic phantom. We subsequently scanned the phantom five times with a routine abdominal CT protocol. Images were reconstructed using iterative reconstruction and two soft tissue kernels and one bone kernel. Radiomics features were extracted and assessed for repeatability and susceptibility towards image reconstruction settings using concordance correlation coefficients. RESULTS Our analysis revealed 19 of 86 features (22 %) as highly repeatable (CCC ≥ 0.85) with low susceptibility towards image reconstruction protocols. Most features analyzed depicted critical non-repeatability with CCC's < 0.75 even under entirely consistent imaging acquisition settings. Edge enhancing kernels result in higher variances between the scans and differences in repeatability and reproducibility were detected between PSMA-positive and negative lymph nodes with overall more stable features seen in tumor positive lymph nodes. CONCLUSIONS Both, repeatability and reproducibility play a crucial role in the validation process of radiomics features in clinical routine. This phantom study shows that most radiomics features in contrast to previous studies, including phantom and clinical, do not depict sufficient intra-scanner repeatability to serve as reliable diagnostic tools.
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Affiliation(s)
- Hanna Muenzfeld
- Department of Radiology, Charité - Universitätsmedizin Berlin, Germany.
| | - Claus Nowak
- Institute of Biometry and Clinical Epidemiology, Charité - Universitätsmedizin Berlin, Germany; Berlin Institute of Health, Berlin, Germany
| | | | | | - Bernd Hamm
- Department of Radiology, Charité - Universitätsmedizin Berlin, Germany
| | - Paul Jahnke
- Department of Radiology, Charité - Universitätsmedizin Berlin, Germany
| | - Tobias Penzkofer
- Department of Radiology, Charité - Universitätsmedizin Berlin, Germany; Berlin Institute of Health, Berlin, Germany
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Moura Cunha G, Chernyak V, Fowler KJ, Sirlin CB. Up-to-Date Role of CT/MRI LI-RADS in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2021; 8:513-527. [PMID: 34104640 PMCID: PMC8180267 DOI: 10.2147/jhc.s268288] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/01/2021] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of mortality worldwide and a major healthcare burden in most societies. Computed tomography (CT) and magnetic resonance imaging (MRI) play a pivotal role in the medical care of patients with or at risk for hepatocellular carcinoma (HCC). When stringent imaging criteria are fulfilled, CT and MRI allow for diagnosis, staging, and assessment of response to treatment, without the need for invasive workup, and can inform clinical decision making. Owing to the central role of these imaging modalities in HCC management, standardization is essential to facilitate proper imaging technique, accurate interpretation, and clear communication among all stakeholders in both the clinical practice and research settings. The Liver Imaging Reporting and Data System (LI-RADS) is a comprehensive system that provides standardization across the continuum of HCC imaging, including ordinal probabilistic approach for reporting that directs individualized management. This review discusses the up-to-date role of CT and MRI in HCC imaging from the LI-RADS perspective. It also provides a glimpse into the future by discussing how advances in knowledge and technology are likely to enrich the LI-RADS approach.
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Affiliation(s)
- Guilherme Moura Cunha
- Liver Imaging Group, Department of Radiology, University of California San Diego, La Jolla, CA, USA
| | - Victoria Chernyak
- Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kathryn J Fowler
- Liver Imaging Group, Department of Radiology, University of California San Diego, La Jolla, CA, USA
| | - Claude B Sirlin
- Liver Imaging Group, Department of Radiology, University of California San Diego, La Jolla, CA, USA
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Halligan S, Menu Y, Mallett S. Why did European Radiology reject my radiomic biomarker paper? How to correctly evaluate imaging biomarkers in a clinical setting. Eur Radiol 2021; 31:9361-9368. [PMID: 34003349 PMCID: PMC8589811 DOI: 10.1007/s00330-021-07971-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/06/2021] [Accepted: 03/31/2021] [Indexed: 12/23/2022]
Abstract
This review explains in simple terms, accessible to the non-statistician, general principles regarding the correct research methods to develop and then evaluate imaging biomarkers in a clinical setting, including radiomic biomarkers. The distinction between diagnostic and prognostic biomarkers is made and emphasis placed on the need to assess clinical utility within the context of a multivariable model. Such models should not be restricted to imaging biomarkers and must include relevant disease and patient characteristics likely to be clinically useful. Biomarker utility is based on whether its addition to the basic clinical model improves diagnosis or prediction. Approaches to both model development and evaluation are explained and the need for adequate amounts of representative data stressed so as to avoid underpowering and overfitting. Advice is provided regarding how to report the research correctly. KEY POINTS: • Imaging biomarker research is common but methodological errors are encountered frequently that may mean the research is not clinically useful. • The clinical utility of imaging biomarkers is best assessed by their additive effect on multivariable models based on clinical factors known to be important. • The data used to develop such models should be sufficient for the number of variables investigated and the model should be evaluated, preferably using data unrelated to development.
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Affiliation(s)
- Steve Halligan
- Centre for Medical Imaging, University College London UCL, 43-45 Foley Street, London, W1W 7TS, UK.
| | - Yves Menu
- Department of Diagnostic and Interventional Radiology, Saint Antoine Hospital, APHP-Sorbonne University, Paris, France
| | - Sue Mallett
- Centre for Medical Imaging, University College London UCL, 43-45 Foley Street, London, W1W 7TS, UK
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80
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El Ayachy R, Giraud N, Giraud P, Durdux C, Giraud P, Burgun A, Bibault JE. The Role of Radiomics in Lung Cancer: From Screening to Treatment and Follow-Up. Front Oncol 2021; 11:603595. [PMID: 34026602 PMCID: PMC8131863 DOI: 10.3389/fonc.2021.603595] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Lung cancer represents the first cause of cancer-related death in the world. Radiomics studies arise rapidly in this late decade. The aim of this review is to identify important recent publications to be synthesized into a comprehensive review of the current status of radiomics in lung cancer at each step of the patients' care. METHODS A literature review was conducted using PubMed/Medline for search of relevant peer-reviewed publications from January 2012 to June 2020. RESULTS We identified several studies at each point of patient's care: detection and classification of lung nodules (n=16), determination of histology and genomic (n=10) and finally treatment outcomes predictions (=23). We reported the methodology of those studies and their results and discuss the limitations and the progress to be made for clinical routine applications. CONCLUSION Promising perspectives arise from machine learning applications and radiomics based models in lung cancers, yet further data are necessary for their implementation in daily care. Multicentric collaboration and attention to quality and reproductivity of radiomics studies should be further consider.
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Affiliation(s)
- Radouane El Ayachy
- Radiation Oncology Department, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
- Cancer Research and Personalized Medicine-Integrated Cancer Research Center (SIRIC), Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
- INSERM UMR 1138 Team 22: Information Sciences to support Personalized Medicine, Cordeliers Research Centre, Paris Descartes University, Paris, France
| | - Nicolas Giraud
- INSERM UMR 1138 Team 22: Information Sciences to support Personalized Medicine, Cordeliers Research Centre, Paris Descartes University, Paris, France
- Radiation Oncology Department, Haut-Lévêque Hospital, CHU de Bordeaux, Pessac, France
| | - Paul Giraud
- Radiation Oncology Department, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
- Cancer Research and Personalized Medicine-Integrated Cancer Research Center (SIRIC), Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
- INSERM UMR 1138 Team 22: Information Sciences to support Personalized Medicine, Cordeliers Research Centre, Paris Descartes University, Paris, France
| | - Catherine Durdux
- Radiation Oncology Department, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
- Cancer Research and Personalized Medicine-Integrated Cancer Research Center (SIRIC), Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Philippe Giraud
- Radiation Oncology Department, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
- Cancer Research and Personalized Medicine-Integrated Cancer Research Center (SIRIC), Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Anita Burgun
- Cancer Research and Personalized Medicine-Integrated Cancer Research Center (SIRIC), Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
- INSERM UMR 1138 Team 22: Information Sciences to support Personalized Medicine, Cordeliers Research Centre, Paris Descartes University, Paris, France
| | - Jean Emmanuel Bibault
- Radiation Oncology Department, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
- Cancer Research and Personalized Medicine-Integrated Cancer Research Center (SIRIC), Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
- INSERM UMR 1138 Team 22: Information Sciences to support Personalized Medicine, Cordeliers Research Centre, Paris Descartes University, Paris, France
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81
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Slart RHJA, Williams MC, Juarez-Orozco LE, Rischpler C, Dweck MR, Glaudemans AWJM, Gimelli A, Georgoulias P, Gheysens O, Gaemperli O, Habib G, Hustinx R, Cosyns B, Verberne HJ, Hyafil F, Erba PA, Lubberink M, Slomka P, Išgum I, Visvikis D, Kolossváry M, Saraste A. Position paper of the EACVI and EANM on artificial intelligence applications in multimodality cardiovascular imaging using SPECT/CT, PET/CT, and cardiac CT. Eur J Nucl Med Mol Imaging 2021; 48:1399-1413. [PMID: 33864509 PMCID: PMC8113178 DOI: 10.1007/s00259-021-05341-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/25/2021] [Indexed: 12/18/2022]
Abstract
In daily clinical practice, clinicians integrate available data to ascertain the diagnostic and prognostic probability of a disease or clinical outcome for their patients. For patients with suspected or known cardiovascular disease, several anatomical and functional imaging techniques are commonly performed to aid this endeavor, including coronary computed tomography angiography (CCTA) and nuclear cardiology imaging. Continuous improvement in positron emission tomography (PET), single-photon emission computed tomography (SPECT), and CT hardware and software has resulted in improved diagnostic performance and wide implementation of these imaging techniques in daily clinical practice. However, the human ability to interpret, quantify, and integrate these data sets is limited. The identification of novel markers and application of machine learning (ML) algorithms, including deep learning (DL) to cardiovascular imaging techniques will further improve diagnosis and prognostication for patients with cardiovascular diseases. The goal of this position paper of the European Association of Nuclear Medicine (EANM) and the European Association of Cardiovascular Imaging (EACVI) is to provide an overview of the general concepts behind modern machine learning-based artificial intelligence, highlights currently prefered methods, practices, and computational models, and proposes new strategies to support the clinical application of ML in the field of cardiovascular imaging using nuclear cardiology (hybrid) and CT techniques.
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Affiliation(s)
- Riemer H J A Slart
- Medical Imaging Centre, Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Hanzeplein 1, PO 9700 RB, Groningen, The Netherlands.
- Faculty of Science and Technology Biomedical, Photonic Imaging, University of Twente, Enschede, The Netherlands.
| | - Michelle C Williams
- British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
- Edinburgh Imaging facility QMRI, Edinburgh, UK
| | - Luis Eduardo Juarez-Orozco
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Christoph Rischpler
- Department of Nuclear Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Marc R Dweck
- British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
- Edinburgh Imaging facility QMRI, Edinburgh, UK
| | - Andor W J M Glaudemans
- Medical Imaging Centre, Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Hanzeplein 1, PO 9700 RB, Groningen, The Netherlands
| | | | - Panagiotis Georgoulias
- Department of Nuclear Medicine, Faculty of Medicine, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Olivier Gheysens
- Department of Nuclear Medicine, Cliniques Universitaires Saint-Luc and Institute of Clinical and Experimental Research (IREC), Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | | | - Gilbert Habib
- APHM, Cardiology Department, La Timone Hospital, Marseille, France
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, Marseille, France
| | - Roland Hustinx
- Division of Nuclear Medicine and Oncological Imaging, Department of Medical Physics, ULiège, Liège, Belgium
| | - Bernard Cosyns
- Department of Cardiology, Centrum voor Hart en Vaatziekten, Universitair Ziekenhuis Brussel, 101 Laarbeeklaan, 1090, Brussels, Belgium
| | - Hein J Verberne
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Fabien Hyafil
- Department of Nuclear Medicine, DMU IMAGINA, Georges-Pompidou European Hospital, Assistance Publique - Hôpitaux de Paris, F-75015, Paris, France
- University of Paris, PARCC, INSERM, F-75006, Paris, France
| | - Paola A Erba
- Medical Imaging Centre, Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Hanzeplein 1, PO 9700 RB, Groningen, The Netherlands
- Department of Nuclear Medicine (P.A.E.), University of Pisa, Pisa, Italy
- Department of Translational Research and New Technology in Medicine (P.A.E.), University of Pisa, Pisa, Italy
| | - Mark Lubberink
- Department of Surgical Sciences/Radiology, Uppsala University, Uppsala, Sweden
- Medical Physics, Uppsala University Hospital, Uppsala, Sweden
| | - Piotr Slomka
- Department of Imaging, Medicine, and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ivana Išgum
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Biomedical Engineering and Physics, Amsterdam UMC - location AMC, University of Amsterdam, 1105, Amsterdam, AZ, Netherlands
| | | | - Márton Kolossváry
- MTA-SE Cardiovascular Imaging Research Group, Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, Hungary
| | - Antti Saraste
- Turku PET Centre, Turku University Hospital, University of Turku, Turku, Finland
- Heart Center, Turku University Hospital, Turku, Finland
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82
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COVID-19 pathophysiology may be driven by an imbalance in the renin-angiotensin-aldosterone system. Nat Commun 2021; 12:2417. [PMID: 33893295 PMCID: PMC8065208 DOI: 10.1038/s41467-021-22713-z|] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
SARS-CoV-2 uses ACE2, an inhibitor of the Renin-Angiotensin-Aldosterone System (RAAS), for cellular entry. Studies indicate that RAAS imbalance worsens the prognosis in COVID-19. We present a consecutive retrospective COVID-19 cohort with findings of frequent pulmonary thromboembolism (17%), high pulmonary artery pressure (60%) and lung MRI perfusion disturbances. We demonstrate, in swine, that infusing angiotensin II or blocking ACE2 induces increased pulmonary artery pressure, reduces blood oxygenation, increases coagulation, disturbs lung perfusion, induces diffuse alveolar damage, and acute tubular necrosis compared to control animals. We further demonstrate that this imbalanced state can be ameliorated by infusion of an angiotensin receptor blocker and low-molecular-weight heparin. In this work, we show that a pathophysiological state in swine induced by RAAS imbalance shares several features with the clinical COVID-19 presentation. Therefore, we propose that severe COVID-19 could partially be driven by a RAAS imbalance.
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83
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Duclos V, Iep A, Gomez L, Goldfarb L, Besson FL. PET Molecular Imaging: A Holistic Review of Current Practice and Emerging Perspectives for Diagnosis, Therapeutic Evaluation and Prognosis in Clinical Oncology. Int J Mol Sci 2021; 22:4159. [PMID: 33923839 PMCID: PMC8073681 DOI: 10.3390/ijms22084159] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
PET/CT molecular imaging has been imposed in clinical oncological practice over the past 20 years, driven by its two well-grounded foundations: quantification and radiolabeled molecular probe vectorization. From basic visual interpretation to more sophisticated full kinetic modeling, PET technology provides a unique opportunity to characterize various biological processes with different levels of analysis. In clinical practice, many efforts have been made during the last two decades to standardize image analyses at the international level, but advanced metrics are still under use in practice. In parallel, the integration of PET imaging with radionuclide therapy, also known as radiolabeled theranostics, has paved the way towards highly sensitive radionuclide-based precision medicine, with major breakthroughs emerging in neuroendocrine tumors and prostate cancer. PET imaging of tumor immunity and beyond is also emerging, emphasizing the unique capabilities of PET molecular imaging to constantly adapt to emerging oncological challenges. However, these new horizons face the growing complexity of multidimensional data. In the era of precision medicine, statistical and computer sciences are currently revolutionizing image-based decision making, paving the way for more holistic cancer molecular imaging analyses at the whole-body level.
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Affiliation(s)
- Valentin Duclos
- Department of Biophysics and Nuclear Medicine-Molecular Imaging, Hôpitaux Universitaires Paris Saclay, Assistance Publique-Hôpitaux de Paris, CHU Bicêtre, 94270 Le Kremlin-Bicêtre, France; (V.D.); (A.I.); (L.G.)
| | - Alex Iep
- Department of Biophysics and Nuclear Medicine-Molecular Imaging, Hôpitaux Universitaires Paris Saclay, Assistance Publique-Hôpitaux de Paris, CHU Bicêtre, 94270 Le Kremlin-Bicêtre, France; (V.D.); (A.I.); (L.G.)
| | - Léa Gomez
- Department of Biophysics and Nuclear Medicine-Molecular Imaging, Hôpitaux Universitaires Paris Saclay, Assistance Publique-Hôpitaux de Paris, CHU Bicêtre, 94270 Le Kremlin-Bicêtre, France; (V.D.); (A.I.); (L.G.)
| | - Lucas Goldfarb
- Service Hospitalier Frédéric Joliot-CEA, 91401 Orsay, France;
| | - Florent L. Besson
- Department of Biophysics and Nuclear Medicine-Molecular Imaging, Hôpitaux Universitaires Paris Saclay, Assistance Publique-Hôpitaux de Paris, CHU Bicêtre, 94270 Le Kremlin-Bicêtre, France; (V.D.); (A.I.); (L.G.)
- Université Paris Saclay, CEA, CNRS, Inserm, BioMaps, 91401 Orsay, France
- School of Medicine, Université Paris Saclay, 94720 Le Kremlin-Bicêtre, France
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84
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Cuocolo R, Imbriaco M. Machine learning solutions in radiology: does the emperor have no clothes? Eur Radiol 2021; 31:3783-3785. [PMID: 33856518 DOI: 10.1007/s00330-021-07895-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/25/2023]
Abstract
KEY POINTS • Interest in radiomics and machine learning is steadily increasing and is reflected both in research output and number of commercially available solutions.• Currently available commercial products using machine learning are often supported by limited evidence of clinical usefulness and studies are often of low methodological quality.• Ethical and regulatory issues remain open and hinder implementation of machine learning software packages in daily clinical practice.
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Affiliation(s)
- Renato Cuocolo
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", via Pansini 5, 80131, Naples, Italy. .,Augmented Reality for Health Monitoring Laboratory (ARHeMLab), Department of Electrical Engineering and Information Technology, University of Naples "Federico II", Naples, Italy.
| | - Massimo Imbriaco
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Naples, Italy
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85
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Wang J. Editorial for "The nomogram of MRI-based radiomics with complementary visual features by machine learning improves stratification of glioblastoma patients: A multicenter study". J Magn Reson Imaging 2021; 54:584-585. [PMID: 33751733 DOI: 10.1002/jmri.27572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jinnan Wang
- Department of Radiology, University of Washington, Seattle, Washington, USA.,Siemens Medical Solutions, Seattle, Washington, USA
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86
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Artificial intelligence: Deep learning in oncological radiomics and challenges of interpretability and data harmonization. Phys Med 2021; 83:108-121. [PMID: 33765601 DOI: 10.1016/j.ejmp.2021.03.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
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87
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Dietzel M, Clauser P, Kapetas P, Schulz-Wendtland R, Baltzer PAT. Images Are Data: A Breast Imaging Perspective on a Contemporary Paradigm. ROFO-FORTSCHR RONTG 2021; 193:898-908. [PMID: 33535260 DOI: 10.1055/a-1346-0095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Considering radiological examinations not as mere images, but as a source of data, has become the key paradigm in the diagnostic imaging field. This change of perspective is particularly popular in breast imaging. It allows breast radiologists to apply algorithms derived from computer science, to realize innovative clinical applications, and to refine already established methods. In this context, the terminology "imaging biomarker", "radiomics", and "artificial intelligence" are of pivotal importance. These methods promise noninvasive, low-cost (e. g., in comparison to multigene arrays), and workflow-friendly (automated, only one examination, instantaneous results, etc.) delivery of clinically relevant information. METHODS AND RESULTS This paper is designed as a narrative review on the previously mentioned paradigm. The focus is on key concepts in breast imaging and important buzzwords are explained. For all areas of breast imaging, exemplary studies and potential clinical use cases are discussed. CONCLUSION Considering radiological examination as a source of data may optimize patient management by guiding individualized breast cancer diagnosis and oncologic treatment in the age of precision medicine. KEY POINTS · In conventional breast imaging, examinations are interpreted based on patterns perceivable by visual inspection.. · The radiomics paradigm treats breast images as a source of data, containing information beyond what is visible to our eyes.. · This results in radiomic signatures that may be considered as imaging biomarkers, as they provide diagnostic, predictive, and prognostic information.. · Radiomics derived imaging biomarkers may be used to individualize breast cancer treatment in the era of precision medicine.. · The concept and key research of radiomics in the field of breast imaging will be discussed in this narrative review.. CITATION FORMAT · Dietzel M, Clauser P, Kapetas P et al. Images Are Data: A Breast Imaging Perspective on a Contemporary Paradigm. Fortschr Röntgenstr 2021; 193: 898 - 908.
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Affiliation(s)
| | - Paola Clauser
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Molecular and Gender Imaging, Medical University Vienna, Vienna, Austria
| | - Panagiotis Kapetas
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Molecular and Gender Imaging, Medical University Vienna, Vienna, Austria
| | | | - Pascal Andreas Thomas Baltzer
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Molecular and Gender Imaging, Medical University Vienna, Vienna, Austria
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88
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[Artificial intelligence in breast imaging : Areas of application from a clinical perspective]. Radiologe 2021; 61:192-198. [PMID: 33507318 PMCID: PMC7851036 DOI: 10.1007/s00117-020-00802-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2020] [Indexed: 12/22/2022]
Abstract
Klinisches/methodisches Problem Bei der Mammadiagnostik gilt es, klinische sowie multimodal bildgebende Informationen mit perkutanen und operativen Eingriffen zu koordinieren. Aus dieser Komplexität entsteht eine Reihe von Problemen: übersehene Karzinome, Überdiagnose, falsch-positive Befunde, unnötige weiterführende Bildgebung, Biopsien und Operationen. Radiologische Standardverfahren Folgende Untersuchungsverfahren werden in der Mammadiagnostik eingesetzt: Röntgenmammographie, Tomosynthese, kontrastangehobene Mammographie, (multiparametrischer) Ultraschall, Magnetresonanztomographie, Computertomographie, nuklearmedizinische Verfahren sowie deren Hybridvarianten. Methodische Innovationen Künstliche Intelligenz (KI) verspricht Abhilfe bei praktisch allen Problemen der Mammadiagnostik. Potenziell lassen sich Fehlbefunde vermeiden, bildgebende Verfahren effizienter einsetzen und möglicherweise auch biologische Phänotypen von Mammakarzinomen definieren. Leistungsfähigkeit Auf KI basierende Software wird für zahlreiche Anwendungen entwickelt. Am weitesten fortgeschritten sind Systeme für das Screening mittels Mammographie. Probleme sind monozentrische sowie kurzfristig am finanziellen Erfolg orientierte Ansätze. Bewertung Künstliche Intelligenz (KI) verspricht eine Verbesserung der Mammadiagnostik. Durch die Vereinfachung von Abläufen, die Reduktion monotoner und ergebnisloser Tätigkeiten und den Hinweis auf mögliche Fehler ist eine Beschleunigung von dann weitgehend fehlerfreien Abläufen denkbar. Empfehlung für die Praxis In diesem Beitrag werden die Anforderungen der Mammadiagnostik und mögliche Einsatzgebiete der der KI beleuchtet. Je nach Definition gibt es bereits praktisch anwendbare Softwaretools für die Mammadiagnostik. Globale Lösungen stehen allerdings noch aus.
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89
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Radiomics for prediction of survival in lower-grade gliomas-it's time to move beyond the crystal ball. Eur Radiol 2020; 31:1783-1784. [PMID: 33341906 PMCID: PMC7979609 DOI: 10.1007/s00330-020-07603-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/04/2020] [Indexed: 11/26/2022]
Abstract
• Radiomics might help predict survival of patients with lower-grade gliomas. • Several different models using different radiomics features have been proposed with only little overlap in included features. • Prospective trials and validation studies are needed to establish which models offer clinical benefit and which do not.
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