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Mansouri Z, Salimi Y, Akhavanallaf A, Shiri I, Teixeira EPA, Hou X, Beauregard JM, Rahmim A, Zaidi H. Deep transformer-based personalized dosimetry from SPECT/CT images: a hybrid approach for [ 177Lu]Lu-DOTATATE radiopharmaceutical therapy. Eur J Nucl Med Mol Imaging 2024; 51:1516-1529. [PMID: 38267686 DOI: 10.1007/s00259-024-06618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/15/2024] [Indexed: 01/26/2024]
Abstract
PURPOSE Accurate dosimetry is critical for ensuring the safety and efficacy of radiopharmaceutical therapies. In current clinical dosimetry practice, MIRD formalisms are widely employed. However, with the rapid advancement of deep learning (DL) algorithms, there has been an increasing interest in leveraging the calculation speed and automation capabilities for different tasks. We aimed to develop a hybrid transformer-based deep learning (DL) model that incorporates a multiple voxel S-value (MSV) approach for voxel-level dosimetry in [177Lu]Lu-DOTATATE therapy. The goal was to enhance the performance of the model to achieve accuracy levels closely aligned with Monte Carlo (MC) simulations, considered as the standard of reference. We extended our analysis to include MIRD formalisms (SSV and MSV), thereby conducting a comprehensive dosimetry study. METHODS We used a dataset consisting of 22 patients undergoing up to 4 cycles of [177Lu]Lu-DOTATATE therapy. MC simulations were used to generate reference absorbed dose maps. In addition, MIRD formalism approaches, namely, single S-value (SSV) and MSV techniques, were performed. A UNEt TRansformer (UNETR) DL architecture was trained using five-fold cross-validation to generate MC-based dose maps. Co-registered CT images were fed into the network as input, whereas the difference between MC and MSV (MC-MSV) was set as output. DL results are then integrated to MSV to revive the MC dose maps. Finally, the dose maps generated by MSV, SSV, and DL were quantitatively compared to the MC reference at both voxel level and organ level (organs at risk and lesions). RESULTS The DL approach showed slightly better performance (voxel relative absolute error (RAE) = 5.28 ± 1.32) compared to MSV (voxel RAE = 5.54 ± 1.4) and outperformed SSV (voxel RAE = 7.8 ± 3.02). Gamma analysis pass rates were 99.0 ± 1.2%, 98.8 ± 1.3%, and 98.7 ± 1.52% for DL, MSV, and SSV approaches, respectively. The computational time for MC was the highest (~2 days for a single-bed SPECT study) compared to MSV, SSV, and DL, whereas the DL-based approach outperformed the other approaches in terms of time efficiency (3 s for a single-bed SPECT). Organ-wise analysis showed absolute percent errors of 1.44 ± 3.05%, 1.18 ± 2.65%, and 1.15 ± 2.5% for SSV, MSV, and DL approaches, respectively, in lesion-absorbed doses. CONCLUSION A hybrid transformer-based deep learning model was developed for fast and accurate dose map generation, outperforming the MIRD approaches, specifically in heterogenous regions. The model achieved accuracy close to MC gold standard and has potential for clinical implementation for use on large-scale datasets.
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Affiliation(s)
- Zahra Mansouri
- Division of Nuclear Medicine and Molecular Imaging, Department of Medical Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Department of Medical Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular Imaging, Department of Medical Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Department of Medical Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Eliluane Pirazzo Andrade Teixeira
- Division of Nuclear Medicine and Molecular Imaging, Department of Medical Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Xinchi Hou
- Department of Radiology, University of British Columbia, Vancouver, BC, Canada
| | - Jean-Mathieu Beauregard
- Cancer Research Centre and Department of Radiology and Nuclear Medicine, Université Laval, Quebec City, QC, Canada
| | - Arman Rahmim
- Department of Radiology, University of British Columbia, Vancouver, BC, Canada
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Department of Medical Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland.
- Department of Nuclear Medicine, University Medical Center Groningen, University of Groningen, 9700 RB, Groningen, Netherlands.
- Department of Nuclear Medicine, University of Southern Denmark, DK-500, Odense, Denmark.
- University Research and Innovation Center, Óbuda University, Budapest, Hungary.
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Deevband MR, Mohammadi H, Salimi Y, Mostaar A, Deravi N, Fathi M, Vakili K, Yaghoobpoor S, Ghorbani M, Divband A, Tavakoli M. Introducing fitting models for estimating age-specific dose and effective dose in paediatric patients undergoing head, chest and abdomen-pelvis imaging protocols: a patient study. J Med Radiat Sci 2024. [PMID: 38454637 DOI: 10.1002/jmrs.772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 02/03/2024] [Indexed: 03/09/2024] Open
Abstract
INTRODUCTION Concerns regarding the adverse consequences of radiation have increased due to the expanded application of computed tomography (CT) in medical practice. Certain studies have indicated that the radiation dosage depends on the anatomical region, the imaging technique employed and patient-specific variables. The aim of this study is to present fitting models for the estimation of age-specific dose estimates (ASDE), in the same direction of size-specific dose estimates, and effective doses based on patient age, gender and the type of CT examination used in paediatric head, chest and abdomen-pelvis imaging. METHODS A total of 583 paediatric patients were included in the study. Radiometric data were gathered from DICOM files. The patients were categorised into five distinct groups (under 15 years of age), and the effective dose, organ dose and ASDE were computed for the CT examinations involving the head, chest and abdomen-pelvis. Finally, the best fitting models were presented for estimation of ASDE and effective doses based on patient age, gender and the type of examination. RESULTS The ASDE in head, chest, and abdomen-pelvis CT examinations increases with increasing age. As age increases, the effective dose in head and abdomen-pelvis CT scans decreased. However, for chest scans, the effective dose initially showed a decreasing trend until the first year of life; after that, it increases in correlation with age. CONCLUSIONS Based on the presented fitting model for the ASDE, these CT scan quantities depend on factors such as patient age and the type of CT examination. For the effective dose, the gender was also included in the fitting model. By utilising the information about the scan type, region and age, it becomes feasible to estimate the ASDE and effective dose using the models provided in this study.
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Affiliation(s)
- Mohammad Reza Deevband
- Department of Medical Physics and Biomedical Engineering, Faculty of Medicine, Shahid Beheshti University of Medical Sciences and Health Services, Tehran, Iran
| | - Habib Mohammadi
- Department of Medical Physics and Biomedical Engineering, Faculty of Medicine, Shahid Beheshti University of Medical Sciences and Health Services, Tehran, Iran
| | - Yazdan Salimi
- Department of Medical Physics and Biomedical Engineering, Faculty of Medicine, Shahid Beheshti University of Medical Sciences and Health Services, Tehran, Iran
| | - Ahmad Mostaar
- Department of Medical Physics and Biomedical Engineering, Faculty of Medicine, Shahid Beheshti University of Medical Sciences and Health Services, Tehran, Iran
| | - Niloofar Deravi
- Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mobina Fathi
- Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Vakili
- Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shirin Yaghoobpoor
- Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Ghorbani
- Department of Medical Physics and Biomedical Engineering, Faculty of Medicine, Shahid Beheshti University of Medical Sciences and Health Services, Tehran, Iran
| | - Abolhasan Divband
- Department of Pediatrics, Faculty of Medicine, College/Hormozgan University of Medical Science, Bandar Abbas, Iran
| | - Meysam Tavakoli
- Department of Radiation Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
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Shiri I, Salimi Y, Sirjani N, Razeghi B, Bagherieh S, Pakbin M, Mansouri Z, Hajianfar G, Avval AH, Askari D, Ghasemian M, Sandoughdaran S, Sohrabi A, Sadati E, Livani S, Iranpour P, Kolahi S, Khosravi B, Bijari S, Sayfollahi S, Atashzar MR, Hasanian M, Shahhamzeh A, Teimouri A, Goharpey N, Shirzad-Aski H, Karimi J, Radmard AR, Rezaei-Kalantari K, Oghli MG, Oveisi M, Vafaei Sadr A, Voloshynovskiy S, Zaidi H. Differential privacy preserved federated learning for prognostic modeling in COVID-19 patients using large multi-institutional chest CT dataset. Med Phys 2024. [PMID: 38335175 DOI: 10.1002/mp.16964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/10/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Notwithstanding the encouraging results of previous studies reporting on the efficiency of deep learning (DL) in COVID-19 prognostication, clinical adoption of the developed methodology still needs to be improved. To overcome this limitation, we set out to predict the prognosis of a large multi-institutional cohort of patients with COVID-19 using a DL-based model. PURPOSE This study aimed to evaluate the performance of deep privacy-preserving federated learning (DPFL) in predicting COVID-19 outcomes using chest CT images. METHODS After applying inclusion and exclusion criteria, 3055 patients from 19 centers, including 1599 alive and 1456 deceased, were enrolled in this study. Data from all centers were split (randomly with stratification respective to each center and class) into a training/validation set (70%/10%) and a hold-out test set (20%). For the DL model, feature extraction was performed on 2D slices, and averaging was performed at the final layer to construct a 3D model for each scan. The DensNet model was used for feature extraction. The model was developed using centralized and FL approaches. For FL, we employed DPFL approaches. Membership inference attack was also evaluated in the FL strategy. For model evaluation, different metrics were reported in the hold-out test sets. In addition, models trained in two scenarios, centralized and FL, were compared using the DeLong test for statistical differences. RESULTS The centralized model achieved an accuracy of 0.76, while the DPFL model had an accuracy of 0.75. Both the centralized and DPFL models achieved a specificity of 0.77. The centralized model achieved a sensitivity of 0.74, while the DPFL model had a sensitivity of 0.73. A mean AUC of 0.82 and 0.81 with 95% confidence intervals of (95% CI: 0.79-0.85) and (95% CI: 0.77-0.84) were achieved by the centralized model and the DPFL model, respectively. The DeLong test did not prove statistically significant differences between the two models (p-value = 0.98). The AUC values for the inference attacks fluctuate between 0.49 and 0.51, with an average of 0.50 ± 0.003 and 95% CI for the mean AUC of 0.500 to 0.501. CONCLUSION The performance of the proposed model was comparable to centralized models while operating on large and heterogeneous multi-institutional datasets. In addition, the model was resistant to inference attacks, ensuring the privacy of shared data during the training process.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Nasim Sirjani
- Research and Development Department, Med Fanavarn Plus Co, Karaj, Iran
| | - Behrooz Razeghi
- Department of Computer Science, University of Geneva, Geneva, Switzerland
| | - Sara Bagherieh
- School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Masoumeh Pakbin
- Imaging Department, Qom University of Medical Sciences, Qom, Iran
| | - Zahra Mansouri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Ghasem Hajianfar
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | | | - Dariush Askari
- Department of Radiology Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Ghasemian
- Department of Radiology, Shahid Beheshti Hospital, Qom University of Medical Sciences, Qom, Iran
| | - Saleh Sandoughdaran
- Department of Clinical Oncology, Royal Surrey County Hospital, Guildford, UK
| | - Ahmad Sohrabi
- Radin Makian Azma Mehr Ltd., Radinmehr Veterinary Laboratory, Iran University of Medical Sciences, Gorgan, Iran
| | - Elham Sadati
- Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Somayeh Livani
- Clinical Research Development Unit (CRDU), Sayad Shirazi Hospital, Golestan University of Medical Sciences, Gorgan, Iran
| | - Pooya Iranpour
- Medical Imaging Research Center, Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shahriar Kolahi
- Department of Radiology, School of Medicine, Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Bardia Khosravi
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Salar Bijari
- Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sahar Sayfollahi
- Department of Neurosurgery, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Atashzar
- Department of Immunology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Mohammad Hasanian
- Department of Radiology, Arak University of Medical Sciences, Arak, Iran
| | - Alireza Shahhamzeh
- Clinical research development center, Qom University of Medical Sciences, Qom, Iran
| | - Arash Teimouri
- Medical Imaging Research Center, Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Goharpey
- Department of radiation oncology, Shohada-e Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Jalal Karimi
- Department of Infectious Disease, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Amir Reza Radmard
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Kiara Rezaei-Kalantari
- Rajaie Cardiovascular, Medical & Research Center, Iran University of Medical Science, Tehran, Iran
| | | | - Mehrdad Oveisi
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alireza Vafaei Sadr
- Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, Pennsylvania, USA
| | | | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark
- University Research and Innovation Center, Óbuda University, Budapest, Hungary
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Shiri I, Razeghi B, Ferdowsi S, Salimi Y, Gündüz D, Teodoro D, Voloshynovskiy S, Zaidi H. PRIMIS: Privacy-preserving medical image sharing via deep sparsifying transform learning with obfuscation. J Biomed Inform 2024; 150:104583. [PMID: 38191010 DOI: 10.1016/j.jbi.2024.104583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 11/19/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
OBJECTIVE The primary objective of our study is to address the challenge of confidentially sharing medical images across different centers. This is often a critical necessity in both clinical and research environments, yet restrictions typically exist due to privacy concerns. Our aim is to design a privacy-preserving data-sharing mechanism that allows medical images to be stored as encoded and obfuscated representations in the public domain without revealing any useful or recoverable content from the images. In tandem, we aim to provide authorized users with compact private keys that could be used to reconstruct the corresponding images. METHOD Our approach involves utilizing a neural auto-encoder. The convolutional filter outputs are passed through sparsifying transformations to produce multiple compact codes. Each code is responsible for reconstructing different attributes of the image. The key privacy-preserving element in this process is obfuscation through the use of specific pseudo-random noise. When applied to the codes, it becomes computationally infeasible for an attacker to guess the correct representation for all the codes, thereby preserving the privacy of the images. RESULTS The proposed framework was implemented and evaluated using chest X-ray images for different medical image analysis tasks, including classification, segmentation, and texture analysis. Additionally, we thoroughly assessed the robustness of our method against various attacks using both supervised and unsupervised algorithms. CONCLUSION This study provides a novel, optimized, and privacy-assured data-sharing mechanism for medical images, enabling multi-party sharing in a secure manner. While we have demonstrated its effectiveness with chest X-ray images, the mechanism can be utilized in other medical images modalities as well.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland; Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Behrooz Razeghi
- Department of Computer Science, University of Geneva, Switzerland; Idiap Research Institute, Switzerland
| | - Sohrab Ferdowsi
- Department of Radiology and Medical Informatics, University of Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Deniz Gündüz
- Department of Electrical and Electronic Engineering, Imperial College London, UK
| | - Douglas Teodoro
- Department of Radiology and Medical Informatics, University of Geneva, Switzerland
| | | | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland; Department of Nuclear Medicine and Molecular Imaging, University of Groningen, The Netherlands; Department of Nuclear Medicine, University of Southern Denmark, Denmark; University Research and Innovation Center, Óbuda University, Budapest, Hungary.
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Mansouri Z, Salimi Y, Amini M, Hajianfar G, Oveisi M, Shiri I, Zaidi H. Development and validation of survival prognostic models for head and neck cancer patients using machine learning and dosiomics and CT radiomics features: a multicentric study. Radiat Oncol 2024; 19:12. [PMID: 38254203 PMCID: PMC10804728 DOI: 10.1186/s13014-024-02409-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND This study aimed to investigate the value of clinical, radiomic features extracted from gross tumor volumes (GTVs) delineated on CT images, dose distributions (Dosiomics), and fusion of CT and dose distributions to predict outcomes in head and neck cancer (HNC) patients. METHODS A cohort of 240 HNC patients from five different centers was obtained from The Cancer Imaging Archive. Seven strategies, including four non-fusion (Clinical, CT, Dose, DualCT-Dose), and three fusion algorithms (latent low-rank representation referred (LLRR),Wavelet, weighted least square (WLS)) were applied. The fusion algorithms were used to fuse the pre-treatment CT images and 3-dimensional dose maps. Overall, 215 radiomics and Dosiomics features were extracted from the GTVs, alongside with seven clinical features incorporated. Five feature selection (FS) methods in combination with six machine learning (ML) models were implemented. The performance of the models was quantified using the concordance index (CI) in one-center-leave-out 5-fold cross-validation for overall survival (OS) prediction considering the time-to-event. RESULTS The mean CI and Kaplan-Meier curves were used for further comparisons. The CoxBoost ML model using the Minimal Depth (MD) FS method and the glmnet model using the Variable hunting (VH) FS method showed the best performance with CI = 0.73 ± 0.15 for features extracted from LLRR fused images. In addition, both glmnet-Cindex and Coxph-Cindex classifiers achieved a CI of 0.72 ± 0.14 by employing the dose images (+ incorporated clinical features) only. CONCLUSION Our results demonstrated that clinical features, Dosiomics and fusion of dose and CT images by specific ML-FS models could predict the overall survival of HNC patients with acceptable accuracy. Besides, the performance of ML methods among the three different strategies was almost comparable.
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Affiliation(s)
- Zahra Mansouri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Mehdi Amini
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Ghasem Hajianfar
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Mehrdad Oveisi
- Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
| | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland.
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
- University Research and Innovation Center, Óbuda University, Budapest, Hungary.
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Salimi Y, Domingo-Fernández D, Hofmann-Apitius M, Birkenbihl C. Data-Driven Thresholding Statistically Biases ATN Profiling across Cohort Datasets. J Prev Alzheimers Dis 2024; 11:185-195. [PMID: 38230732 PMCID: PMC10995057 DOI: 10.14283/jpad.2023.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/02/2023] [Indexed: 01/18/2024]
Abstract
BACKGROUND While the amyloid/tau/neurodegeneration (ATN) framework has found wide application in Alzheimer's disease research, it is unclear if thresholds obtained using distinct thresholding methods are concordant within the same dataset and interchangeable across cohorts. OBJECTIVES To investigate the robustness of data-driven thresholding methods and ATN profiling across cohort datasets. DESIGN AND SETTING We evaluated the impact of thresholding methods on ATN profiles by applying five commonly-used methodologies across cohort datasets. We assessed the generalizability of disease patterns discovered within ATN profiles by clustering individuals from different cohorts who were assigned to the same ATN profile. PARTICIPANTS AND MEASUREMENTS Participants with available CSF amyloid-β 1-42, phosphorylated tau, and total tau measurements were included from eleven AD cohort studies. RESULTS We observed high variability among obtained ATN thresholds, both across methods and datasets that impacted the resulting profile assignments of participants significantly. Clustering participants from different cohorts within the same ATN category indicated that identified disease patterns were comparable across most cohorts and biases introduced through distinct thresholding and data representations remained insignificant in most ATN profiles. CONLUSION Thresholding method selection is a decision of statistical relevance that will inevitably bias the resulting profiling and affect its sensitivity and specificity. Thresholds are likely not directly interchangeable between independent cohorts. To apply the ATN framework as an actionable and robust profiling scheme, a comprehensive understanding of the impact of used thresholding methods, their statistical implications, and a validation of results is crucial.
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Affiliation(s)
- Y. Salimi
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, 53757 Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, 53115 Germany
- Schloß Birlinghoven, Sankt Augustin, 53757 Germany
| | - D. Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, 53757 Germany
| | - M. Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, 53757 Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, 53115 Germany
| | - C. Birkenbihl
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, 53757 Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, 53115 Germany
- Schloß Birlinghoven, Sankt Augustin, 53757 Germany
| | - the Alzheimer’s Disease Neuroimaging Initiative
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, 53757 Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, 53115 Germany
- Schloß Birlinghoven, Sankt Augustin, 53757 Germany
| | - the Japanese Alzheimer’s Disease Neuroimaging Initiative
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, 53757 Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, 53115 Germany
- Schloß Birlinghoven, Sankt Augustin, 53757 Germany
| | - the Alzheimer’s Disease Repository Without Borders Investigators
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, 53757 Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, 53115 Germany
- Schloß Birlinghoven, Sankt Augustin, 53757 Germany
| | - the European Prevention of Alzheimer’s Disease (EPAD) Consortium
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, 53757 Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, 53115 Germany
- Schloß Birlinghoven, Sankt Augustin, 53757 Germany
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Shiri I, Amini M, Yousefirizi F, Vafaei Sadr A, Hajianfar G, Salimi Y, Mansouri Z, Jenabi E, Maghsudi M, Mainta I, Becker M, Rahmim A, Zaidi H. Information fusion for fully automated segmentation of head and neck tumors from PET and CT images. Med Phys 2024; 51:319-333. [PMID: 37475591 DOI: 10.1002/mp.16615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/16/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND PET/CT images combining anatomic and metabolic data provide complementary information that can improve clinical task performance. PET image segmentation algorithms exploiting the multi-modal information available are still lacking. PURPOSE Our study aimed to assess the performance of PET and CT image fusion for gross tumor volume (GTV) segmentations of head and neck cancers (HNCs) utilizing conventional, deep learning (DL), and output-level voting-based fusions. METHODS The current study is based on a total of 328 histologically confirmed HNCs from six different centers. The images were automatically cropped to a 200 × 200 head and neck region box, and CT and PET images were normalized for further processing. Eighteen conventional image-level fusions were implemented. In addition, a modified U2-Net architecture as DL fusion model baseline was used. Three different input, layer, and decision-level information fusions were used. Simultaneous truth and performance level estimation (STAPLE) and majority voting to merge different segmentation outputs (from PET and image-level and network-level fusions), that is, output-level information fusion (voting-based fusions) were employed. Different networks were trained in a 2D manner with a batch size of 64. Twenty percent of the dataset with stratification concerning the centers (20% in each center) were used for final result reporting. Different standard segmentation metrics and conventional PET metrics, such as SUV, were calculated. RESULTS In single modalities, PET had a reasonable performance with a Dice score of 0.77 ± 0.09, while CT did not perform acceptably and reached a Dice score of only 0.38 ± 0.22. Conventional fusion algorithms obtained a Dice score range of [0.76-0.81] with guided-filter-based context enhancement (GFCE) at the low-end, and anisotropic diffusion and Karhunen-Loeve transform fusion (ADF), multi-resolution singular value decomposition (MSVD), and multi-level image decomposition based on latent low-rank representation (MDLatLRR) at the high-end. All DL fusion models achieved Dice scores of 0.80. Output-level voting-based models outperformed all other models, achieving superior results with a Dice score of 0.84 for Majority_ImgFus, Majority_All, and Majority_Fast. A mean error of almost zero was achieved for all fusions using SUVpeak , SUVmean and SUVmedian . CONCLUSION PET/CT information fusion adds significant value to segmentation tasks, considerably outperforming PET-only and CT-only methods. In addition, both conventional image-level and DL fusions achieve competitive results. Meanwhile, output-level voting-based fusion using majority voting of several algorithms results in statistically significant improvements in the segmentation of HNC.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Mehdi Amini
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Fereshteh Yousefirizi
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Alireza Vafaei Sadr
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
- Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, Hershey, USA
| | - Ghasem Hajianfar
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Zahra Mansouri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Elnaz Jenabi
- Research Center for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Maghsudi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ismini Mainta
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Minerva Becker
- Service of Radiology, Geneva University Hospital, Geneva, Switzerland
| | - Arman Rahmim
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Radiology and Physics, University of British Columbia, Vancouver, Canada
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
- Geneva University Neurocenter, Geneva University, Geneva, Switzerland
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark
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8
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Shiri I, Salimi Y, Maghsudi M, Jenabi E, Harsini S, Razeghi B, Mostafaei S, Hajianfar G, Sanaat A, Jafari E, Samimi R, Khateri M, Sheikhzadeh P, Geramifar P, Dadgar H, Bitrafan Rajabi A, Assadi M, Bénard F, Vafaei Sadr A, Voloshynovskiy S, Mainta I, Uribe C, Rahmim A, Zaidi H. Differential privacy preserved federated transfer learning for multi-institutional 68Ga-PET image artefact detection and disentanglement. Eur J Nucl Med Mol Imaging 2023; 51:40-53. [PMID: 37682303 PMCID: PMC10684636 DOI: 10.1007/s00259-023-06418-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
PURPOSE Image artefacts continue to pose challenges in clinical molecular imaging, resulting in misdiagnoses, additional radiation doses to patients and financial costs. Mismatch and halo artefacts occur frequently in gallium-68 (68Ga)-labelled compounds whole-body PET/CT imaging. Correcting for these artefacts is not straightforward and requires algorithmic developments, given that conventional techniques have failed to address them adequately. In the current study, we employed differential privacy-preserving federated transfer learning (FTL) to manage clinical data sharing and tackle privacy issues for building centre-specific models that detect and correct artefacts present in PET images. METHODS Altogether, 1413 patients with 68Ga prostate-specific membrane antigen (PSMA)/DOTA-TATE (TOC) PET/CT scans from 3 countries, including 8 different centres, were enrolled in this study. CT-based attenuation and scatter correction (CT-ASC) was used in all centres for quantitative PET reconstruction. Prior to model training, an experienced nuclear medicine physician reviewed all images to ensure the use of high-quality, artefact-free PET images (421 patients' images). A deep neural network (modified U2Net) was trained on 80% of the artefact-free PET images to utilize centre-based (CeBa), centralized (CeZe) and the proposed differential privacy FTL frameworks. Quantitative analysis was performed in 20% of the clean data (with no artefacts) in each centre. A panel of two nuclear medicine physicians conducted qualitative assessment of image quality, diagnostic confidence and image artefacts in 128 patients with artefacts (256 images for CT-ASC and FTL-ASC). RESULTS The three approaches investigated in this study for 68Ga-PET imaging (CeBa, CeZe and FTL) resulted in a mean absolute error (MAE) of 0.42 ± 0.21 (CI 95%: 0.38 to 0.47), 0.32 ± 0.23 (CI 95%: 0.27 to 0.37) and 0.28 ± 0.15 (CI 95%: 0.25 to 0.31), respectively. Statistical analysis using the Wilcoxon test revealed significant differences between the three approaches, with FTL outperforming CeBa and CeZe (p-value < 0.05) in the clean test set. The qualitative assessment demonstrated that FTL-ASC significantly improved image quality and diagnostic confidence and decreased image artefacts, compared to CT-ASC in 68Ga-PET imaging. In addition, mismatch and halo artefacts were successfully detected and disentangled in the chest, abdomen and pelvic regions in 68Ga-PET imaging. CONCLUSION The proposed approach benefits from using large datasets from multiple centres while preserving patient privacy. Qualitative assessment by nuclear medicine physicians showed that the proposed model correctly addressed two main challenging artefacts in 68Ga-PET imaging. This technique could be integrated in the clinic for 68Ga-PET imaging artefact detection and disentanglement using multicentric heterogeneous datasets.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
- Department of Cardiology, Inselspital, University of Bern, Bern, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Mehdi Maghsudi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Elnaz Jenabi
- Research Center for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sara Harsini
- BC Cancer Research Institute, Vancouver, BC, Canada
| | - Behrooz Razeghi
- Department of Computer Science, University of Geneva, Geneva, Switzerland
| | - Shayan Mostafaei
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Ghasem Hajianfar
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Amirhossein Sanaat
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Esmail Jafari
- The Persian Gulf Nuclear Medicine Research Center, Department of Nuclear Medicine, Molecular Imaging, and Theranostics, Bushehr Medical University Hospital, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Rezvan Samimi
- Department of Medical Radiation Engineering, Shahid Beheshti University, Tehran, Iran
| | - Maziar Khateri
- Department of Medical Radiation Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Peyman Sheikhzadeh
- Department of Nuclear Medicine, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Parham Geramifar
- Research Center for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Habibollah Dadgar
- Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran
| | - Ahmad Bitrafan Rajabi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
- Echocardiography Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Assadi
- The Persian Gulf Nuclear Medicine Research Center, Department of Nuclear Medicine, Molecular Imaging, and Theranostics, Bushehr Medical University Hospital, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - François Bénard
- BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Radiology, University of British Columbia, Vancouver, BC, Canada
| | - Alireza Vafaei Sadr
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
- Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA
| | | | - Ismini Mainta
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Carlos Uribe
- Department of Radiology, University of British Columbia, Vancouver, BC, Canada
- Molecular Imaging and Therapy, BC Cancer, Vancouver, BC, Canada
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Arman Rahmim
- Department of Radiology, University of British Columbia, Vancouver, BC, Canada
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland.
- Geneva University Neuro Center, Geneva University, Geneva, Switzerland.
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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Norouzi G, Nikdel S, Pirayesh E, Salimi Y, Amoui M, Haghighatkhah H, Ghodsi Rad MA, Javanijouni E, Khoshbakht S. Utility of 99mTc-Sestamibi Heart/Liver Uptake Ratio in Screening Nonalcoholic Fatty Liver Disease During Myocardial Perfusion Imaging. Cancer Biother Radiopharm 2023; 38:663-669. [PMID: 36576502 DOI: 10.1089/cbr.2022.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Purpose: Nonalcoholic fatty liver disease (NAFLD) is the most common chronic hepatic disease worldwide, with functional impairment of the mitochondria occurring from early stages. Technetium-99m methoxy-isobutyl-isonitrile (99mTc-MIBI) is a lipophilic agent trapped in the mitochondria. This study aims to evaluate the utility of 99mTc-MIBI heart/liver uptake ratio in screening for NAFLD during myocardial perfusion imaging (MPI). Methods: Seventy eligible patients underwent a 2-d rest/stress 99mTc-MIBI scan with a 2-min planar image acquired in rest phase, at 30, 60, and 120 min postradiotracer administration. Heart/liver uptake ratio was calculated by placing identical regions of interest on the heart and liver dome. All patients underwent liver ultrasound and were allocated into groups A, having NAFLD; and B, healthy individuals without NAFLD. Results: Mean count per pixel heart/liver ratios gradually increased over time in either group; nonetheless the values were significantly higher in group A, regardless of acquisition timing; with the p-value equal to 0.007, 0.014, and 0.010 at 30, 60, and 120 min, respectively. Conclusion: Determining 99mTc-MIBI heart/liver uptake ratio during rest phase in patients undergoing MPI may be a useful, noninvasive screening method for NAFLD; with no additional cost, radiation burden, or adverse effects in these patients. Trial registration number: IR.SBMU.MSP.REC.1398.308.
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Affiliation(s)
- Ghazal Norouzi
- Department of Nuclear Medicine, Shohada-e Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Clinical Research Development Unit, Shohada-e Tajrish Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara Nikdel
- Department of Nuclear Medicine, Shohada-e Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elahe Pirayesh
- Department of Nuclear Medicine, Shohada-e Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Clinical Research Development Unit, Shohada-e Tajrish Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yazdan Salimi
- Biomedical Engineering and Medical Physics Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahasti Amoui
- Department of Nuclear Medicine, Shohada-e Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Clinical Research Development Unit, Shohada-e Tajrish Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Haghighatkhah
- Clinical Research Development Unit, Shohada-e Tajrish Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Diagnostic Imaging, Shohada-e Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Ghodsi Rad
- Department of Nuclear Medicine, Shohada-e Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Clinical Research Development Unit, Shohada-e Tajrish Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elmira Javanijouni
- School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sepideh Khoshbakht
- Department of Nuclear Medicine, Shohada-e Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Clinical Research Development Unit, Shohada-e Tajrish Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Salimi Y, Akhavanallaf A, Mansouri Z, Shiri I, Zaidi H. Real-time, acquisition parameter-free voxel-wise patient-specific Monte Carlo dose reconstruction in whole-body CT scanning using deep neural networks. Eur Radiol 2023; 33:9411-9424. [PMID: 37368113 PMCID: PMC10667156 DOI: 10.1007/s00330-023-09839-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 06/28/2023]
Abstract
OBJECTIVE We propose a deep learning-guided approach to generate voxel-based absorbed dose maps from whole-body CT acquisitions. METHODS The voxel-wise dose maps corresponding to each source position/angle were calculated using Monte Carlo (MC) simulations considering patient- and scanner-specific characteristics (SP_MC). The dose distribution in a uniform cylinder was computed through MC calculations (SP_uniform). The density map and SP_uniform dose maps were fed into a residual deep neural network (DNN) to predict SP_MC through an image regression task. The whole-body dose maps reconstructed by the DNN and MC were compared in the 11 test cases scanned with two tube voltages through transfer learning with/without tube current modulation (TCM). The voxel-wise and organ-wise dose evaluations, such as mean error (ME, mGy), mean absolute error (MAE, mGy), relative error (RE, %), and relative absolute error (RAE, %), were performed. RESULTS The model performance for the 120 kVp and TCM test set in terms of ME, MAE, RE, and RAE voxel-wise parameters was - 0.0302 ± 0.0244 mGy, 0.0854 ± 0.0279 mGy, - 1.13 ± 1.41%, and 7.17 ± 0.44%, respectively. The organ-wise errors for 120 kVp and TCM scenario averaged over all segmented organs in terms of ME, MAE, RE, and RAE were - 0.144 ± 0.342 mGy, and 0.23 ± 0.28 mGy, - 1.11 ± 2.90%, 2.34 ± 2.03%, respectively. CONCLUSION Our proposed deep learning model is able to generate voxel-level dose maps from a whole-body CT scan with reasonable accuracy suitable for organ-level absorbed dose estimation. CLINICAL RELEVANCE STATEMENT We proposed a novel method for voxel dose map calculation using deep neural networks. This work is clinically relevant since accurate dose calculation for patients can be carried out within acceptable computational time compared to lengthy Monte Carlo calculations. KEY POINTS • We proposed a deep neural network approach as an alternative to Monte Carlo dose calculation. • Our proposed deep learning model is able to generate voxel-level dose maps from a whole-body CT scan with reasonable accuracy, suitable for organ-level dose estimation. • By generating a dose distribution from a single source position, our model can generate accurate and personalized dose maps for a wide range of acquisition parameters.
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Affiliation(s)
- Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Zahra Mansouri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland.
- Geneva University Neurocenter, Geneva University, CH_1205, Geneva, Switzerland.
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
- Department of Nuclear Medicine, University of Southern Denmark, DK-500, Odense, Denmark.
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Shiri I, Salimi Y, Hervier E, Pezzoni A, Sanaat A, Mostafaei S, Rahmim A, Mainta I, Zaidi H. Artificial Intelligence-Driven Single-Shot PET Image Artifact Detection and Disentanglement: Toward Routine Clinical Image Quality Assurance. Clin Nucl Med 2023; 48:1035-1046. [PMID: 37883015 PMCID: PMC10662584 DOI: 10.1097/rlu.0000000000004912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/22/2023] [Indexed: 10/27/2023]
Abstract
PURPOSE Medical imaging artifacts compromise image quality and quantitative analysis and might confound interpretation and misguide clinical decision-making. The present work envisions and demonstrates a new paradigm PET image Quality Assurance NETwork (PET-QA-NET) in which various image artifacts are detected and disentangled from images without prior knowledge of a standard of reference or ground truth for routine PET image quality assurance. METHODS The network was trained and evaluated using training/validation/testing data sets consisting of 669/100/100 artifact-free oncological 18 F-FDG PET/CT images and subsequently fine-tuned and evaluated on 384 (20% for fine-tuning) scans from 8 different PET centers. The developed DL model was quantitatively assessed using various image quality metrics calculated for 22 volumes of interest defined on each scan. In addition, 200 additional 18 F-FDG PET/CT scans (this time with artifacts), generated using both CT-based attenuation and scatter correction (routine PET) and PET-QA-NET, were blindly evaluated by 2 nuclear medicine physicians for the presence of artifacts, diagnostic confidence, image quality, and the number of lesions detected in different body regions. RESULTS Across the volumes of interest of 100 patients, SUV MAE values of 0.13 ± 0.04, 0.24 ± 0.1, and 0.21 ± 0.06 were reached for SUV mean , SUV max , and SUV peak , respectively (no statistically significant difference). Qualitative assessment showed a general trend of improved image quality and diagnostic confidence and reduced image artifacts for PET-QA-NET compared with routine CT-based attenuation and scatter correction. CONCLUSION We developed a highly effective and reliable quality assurance tool that can be embedded routinely to detect and correct for 18 F-FDG PET image artifacts in clinical setting with notably improved PET image quality and quantitative capabilities.
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Affiliation(s)
- Isaac Shiri
- From the Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva
- Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yazdan Salimi
- From the Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva
| | - Elsa Hervier
- From the Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva
| | - Agathe Pezzoni
- From the Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva
| | - Amirhossein Sanaat
- From the Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva
| | - Shayan Mostafaei
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Arman Rahmim
- Departments of Radiology and Physics, University of British Columbia
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Ismini Mainta
- From the Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva
| | - Habib Zaidi
- From the Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva
- Geneva University Neuro Center, Geneva University, Geneva, Switzerland
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark
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12
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Shiri I, Razeghi B, Vafaei Sadr A, Amini M, Salimi Y, Ferdowsi S, Boor P, Gündüz D, Voloshynovskiy S, Zaidi H. Multi-institutional PET/CT image segmentation using federated deep transformer learning. Comput Methods Programs Biomed 2023; 240:107706. [PMID: 37506602 DOI: 10.1016/j.cmpb.2023.107706] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND AND OBJECTIVE Generalizable and trustworthy deep learning models for PET/CT image segmentation necessitates large diverse multi-institutional datasets. However, legal, ethical, and patient privacy issues challenge sharing of datasets between different centers. To overcome these challenges, we developed a federated learning (FL) framework for multi-institutional PET/CT image segmentation. METHODS A dataset consisting of 328 FL (HN) cancer patients who underwent clinical PET/CT examinations gathered from six different centers was enrolled. A pure transformer network was implemented as fully core segmentation algorithms using dual channel PET/CT images. We evaluated different frameworks (single center-based, centralized baseline, as well as seven different FL algorithms) using 68 PET/CT images (20% of each center data). In particular, the implemented FL algorithms include clipping with the quantile estimator (ClQu), zeroing with the quantile estimator (ZeQu), federated averaging (FedAvg), lossy compression (LoCo), robust aggregation (RoAg), secure aggregation (SeAg), and Gaussian differentially private FedAvg with adaptive quantile clipping (GDP-AQuCl). RESULTS The Dice coefficient was 0.80±0.11 for both centralized and SeAg FL algorithms. All FL approaches achieved centralized learning model performance with no statistically significant differences. Among the FL algorithms, SeAg and GDP-AQuCl performed better than the other techniques. However, there was no statistically significant difference. All algorithms, except the center-based approach, resulted in relative errors less than 5% for SUVmax and SUVmean for all FL and centralized methods. Centralized and FL algorithms significantly outperformed the single center-based baseline. CONCLUSIONS The developed FL-based (with centralized method performance) algorithms exhibited promising performance for HN tumor segmentation from PET/CT images.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Behrooz Razeghi
- Department of Computer Science, University of Geneva, Geneva, Switzerland
| | - Alireza Vafaei Sadr
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany; Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USA
| | - Mehdi Amini
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Sohrab Ferdowsi
- Department of Computer Science, University of Geneva, Geneva, Switzerland
| | - Peter Boor
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Deniz Gündüz
- Department of Electrical and Electronic Engineering, Imperial College London, UK
| | | | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland; Geneva University Neurocenter, University of Geneva, Geneva, Switzerland; Department of Nuclear Medicine and Molecular Imaging, University of Groningen, Groningen, The Netherlands; Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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Amini M, Pursamimi M, Hajianfar G, Salimi Y, Saberi A, Mehri-Kakavand G, Nazari M, Ghorbani M, Shalbaf A, Shiri I, Zaidi H. Machine learning-based diagnosis and risk classification of coronary artery disease using myocardial perfusion imaging SPECT: A radiomics study. Sci Rep 2023; 13:14920. [PMID: 37691039 PMCID: PMC10493219 DOI: 10.1038/s41598-023-42142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023] Open
Abstract
This study aimed to investigate the diagnostic performance of machine learning-based radiomics analysis to diagnose coronary artery disease status and risk from rest/stress Myocardial Perfusion Imaging (MPI) single-photon emission computed tomography (SPECT). A total of 395 patients suspicious of coronary artery disease who underwent 2-day stress-rest protocol MPI SPECT were enrolled in this study. The left ventricle myocardium, excluding the cardiac cavity, was manually delineated on rest and stress images to define a volume of interest. Added to clinical features (age, sex, family history, diabetes status, smoking, and ejection fraction), a total of 118 radiomics features, were extracted from rest and stress MPI SPECT images to establish different feature sets, including Rest-, Stress-, Delta-, and Combined-radiomics (all together) feature sets. The data were randomly divided into 80% and 20% subsets for training and testing, respectively. The performance of classifiers built from combinations of three feature selections, and nine machine learning algorithms was evaluated for two different diagnostic tasks, including 1) normal/abnormal (no CAD vs. CAD) classification, and 2) low-risk/high-risk CAD classification. Different metrics, including the area under the ROC curve (AUC), accuracy (ACC), sensitivity (SEN), and specificity (SPE), were reported for models' evaluation. Overall, models built on the Stress feature set (compared to other feature sets), and models to diagnose the second task (compared to task 1 models) revealed better performance. The Stress-mRMR-KNN (feature set-feature selection-classifier) reached the highest performance for task 1 with AUC, ACC, SEN, and SPE equal to 0.61, 0.63, 0.64, and 0.6, respectively. The Stress-Boruta-GB model achieved the highest performance for task 2 with AUC, ACC, SEN, and SPE of 0.79, 0.76, 0.75, and 0.76, respectively. Diabetes status from the clinical feature family, and dependence count non-uniformity normalized, from the NGLDM family, which is representative of non-uniformity in the region of interest were the most frequently selected features from stress feature set for CAD risk classification. This study revealed promising results for CAD risk classification using machine learning models built on MPI SPECT radiomics. The proposed models are helpful to alleviate the labor-intensive MPI SPECT interpretation process regarding CAD status and can potentially expedite the diagnostic process.
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Affiliation(s)
- Mehdi Amini
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Mohamad Pursamimi
- Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghasem Hajianfar
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Abdollah Saberi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Ghazal Mehri-Kakavand
- Department of Medical Physics, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Mostafa Nazari
- Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdi Ghorbani
- Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ahmad Shalbaf
- Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
- Department of Cardiology, Inselspital, University of Bern, Bern, Switzerland
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland.
- University Research and Innovation Center, Obuda University, Budapest, Hungary.
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University of Medical Center Groningen, Groningen, The Netherlands.
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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Riveira-Martin M, Akhavanallaf A, Mansouri Z, Bianchetto Wolf N, Salimi Y, Ricoeur A, Mainta I, Garibotto V, López Medina A, Zaidi H. Predictive value of 99mTc-MAA-based dosimetry in personalized 90Y-SIRT planning for liver malignancies. EJNMMI Res 2023; 13:63. [PMID: 37395912 DOI: 10.1186/s13550-023-01011-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
BACKGROUND Selective internal radiation therapy with 90Y radioembolization aims to selectively irradiate liver tumours by administering radioactive microspheres under the theragnostic assumption that the pre-therapy injection of 99mTc labelled macroaggregated albumin (99mTc-MAA) provides an estimation of the 90Y microspheres biodistribution, which is not always the case. Due to the growing interest in theragnostic dosimetry for personalized radionuclide therapy, a robust relationship between the delivered and pre-treatment radiation absorbed doses is required. In this work, we aim to investigate the predictive value of absorbed dose metrics calculated from 99mTc-MAA (simulation) compared to those obtained from 90Y post-therapy SPECT/CT. RESULTS A total of 79 patients were analysed. Pre- and post-therapy 3D-voxel dosimetry was calculated on 99mTc-MAA and 90Y SPECT/CT, respectively, based on Local Deposition Method. Mean absorbed dose, tumour-to-normal ratio, and absorbed dose distribution in terms of dose-volume histogram (DVH) metrics were obtained and compared for each volume of interest (VOI). Mann-Whitney U-test and Pearson's correlation coefficient were used to assess the correlation between both methods. The effect of the tumoral liver volume on the absorbed dose metrics was also investigated. Strong correlation was found between simulation and therapy mean absorbed doses for all VOIs, although simulation tended to overestimate tumour absorbed doses by 26%. DVH metrics showed good correlation too, but significant differences were found for several metrics, mostly on non-tumoral liver. It was observed that the tumoral liver volume does not significantly affect the differences between simulation and therapy absorbed dose metrics. CONCLUSION This study supports the strong correlation between absorbed dose metrics from simulation and therapy dosimetry based on 90Y SPECT/CT, highlighting the predictive ability of 99mTc-MAA, not only in terms of mean absorbed dose but also of the dose distribution.
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Affiliation(s)
- Mercedes Riveira-Martin
- Genetic Oncology, Radiobiology and Radiointeraction Research Group, Galicia Sur Health Research Institute, Vigo, Spain
- Department of Radiology, Rehabilitation and Physiotherapy, Medicine School, Complutense University of Madrid, Madrid, Spain
| | - Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular Imaging, Diagnostic Department, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Zahra Mansouri
- Division of Nuclear Medicine and Molecular Imaging, Diagnostic Department, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Nicola Bianchetto Wolf
- Division of Nuclear Medicine and Molecular Imaging, Diagnostic Department, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Diagnostic Department, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Alexis Ricoeur
- Service of Radiology, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Ismini Mainta
- Division of Nuclear Medicine and Molecular Imaging, Diagnostic Department, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Valentina Garibotto
- Division of Nuclear Medicine and Molecular Imaging, Diagnostic Department, Geneva University Hospital, 1211, Geneva, Switzerland
- Centre for Biomedical Imaging (CIBM), Geneva, Switzerland
- Geneva Neuroscience Centre, Geneva University, Geneva, Switzerland
| | - Antonio López Medina
- Department of Medical Physics and RP, Hospital do Meixoeiro (GALARIA), Vigo, Spain.
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Diagnostic Department, Geneva University Hospital, 1211, Geneva, Switzerland.
- Geneva Neuroscience Centre, Geneva University, Geneva, Switzerland.
- Department of Nuclear Medicine and Molecular Imaging, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands.
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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15
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Sanaat A, Shooli H, Böhringer AS, Sadeghi M, Shiri I, Salimi Y, Ginovart N, Garibotto V, Arabi H, Zaidi H. A cycle-consistent adversarial network for brain PET partial volume correction without prior anatomical information. Eur J Nucl Med Mol Imaging 2023; 50:1881-1896. [PMID: 36808000 PMCID: PMC10199868 DOI: 10.1007/s00259-023-06152-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/12/2023] [Indexed: 02/23/2023]
Abstract
PURPOSE Partial volume effect (PVE) is a consequence of the limited spatial resolution of PET scanners. PVE can cause the intensity values of a particular voxel to be underestimated or overestimated due to the effect of surrounding tracer uptake. We propose a novel partial volume correction (PVC) technique to overcome the adverse effects of PVE on PET images. METHODS Two hundred and twelve clinical brain PET scans, including 50 18F-Fluorodeoxyglucose (18F-FDG), 50 18F-Flortaucipir, 36 18F-Flutemetamol, and 76 18F-FluoroDOPA, and their corresponding T1-weighted MR images were enrolled in this study. The Iterative Yang technique was used for PVC as a reference or surrogate of the ground truth for evaluation. A cycle-consistent adversarial network (CycleGAN) was trained to directly map non-PVC PET images to PVC PET images. Quantitative analysis using various metrics, including structural similarity index (SSIM), root mean squared error (RMSE), and peak signal-to-noise ratio (PSNR), was performed. Furthermore, voxel-wise and region-wise-based correlations of activity concentration between the predicted and reference images were evaluated through joint histogram and Bland and Altman analysis. In addition, radiomic analysis was performed by calculating 20 radiomic features within 83 brain regions. Finally, a voxel-wise two-sample t-test was used to compare the predicted PVC PET images with reference PVC images for each radiotracer. RESULTS The Bland and Altman analysis showed the largest and smallest variance for 18F-FDG (95% CI: - 0.29, + 0.33 SUV, mean = 0.02 SUV) and 18F-Flutemetamol (95% CI: - 0.26, + 0.24 SUV, mean = - 0.01 SUV), respectively. The PSNR was lowest (29.64 ± 1.13 dB) for 18F-FDG and highest (36.01 ± 3.26 dB) for 18F-Flutemetamol. The smallest and largest SSIM were achieved for 18F-FDG (0.93 ± 0.01) and 18F-Flutemetamol (0.97 ± 0.01), respectively. The average relative error for the kurtosis radiomic feature was 3.32%, 9.39%, 4.17%, and 4.55%, while it was 4.74%, 8.80%, 7.27%, and 6.81% for NGLDM_contrast feature for 18F-Flutemetamol, 18F-FluoroDOPA, 18F-FDG, and 18F-Flortaucipir, respectively. CONCLUSION An end-to-end CycleGAN PVC method was developed and evaluated. Our model generates PVC images from the original non-PVC PET images without requiring additional anatomical information, such as MRI or CT. Our model eliminates the need for accurate registration or segmentation or PET scanner system response characterization. In addition, no assumptions regarding anatomical structure size, homogeneity, boundary, or background level are required.
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Affiliation(s)
- Amirhossein Sanaat
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Hossein Shooli
- Persian Gulf Nuclear Medicine Research Center, Department of Molecular Imaging and Radionuclide Therapy (MIRT), Bushehr Medical University Hospital, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Andrew Stephen Böhringer
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Maryam Sadeghi
- Department of Medical Statistics, Informatics and Health Economics, Medical University of Innsbruck, Schoepfstr. 41, Innsbruck, Austria
| | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Nathalie Ginovart
- Geneva University Neurocenter, University of Geneva, Geneva, Switzerland
- Department of Psychiatry, Geneva University, Geneva, Switzerland
- Department of Basic Neuroscience, Geneva University, Geneva, Switzerland
| | - Valentina Garibotto
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
- Geneva University Neurocenter, University of Geneva, Geneva, Switzerland
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland.
- Geneva University Neurocenter, University of Geneva, Geneva, Switzerland.
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, Groningen, Netherlands.
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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Andrearczyk V, Oreiller V, Abobakr M, Akhavanallaf A, Balermpas P, Boughdad S, Capriotti L, Castelli J, Le Rest CC, Decazes P, Correia R, El-Habashy D, Elhalawani H, Fuller CD, Jreige M, Khamis Y, La Greca A, Mohamed A, Naser M, Prior JO, Ruan S, Tanadini-Lang S, Tankyevych O, Salimi Y, Vallières M, Vera P, Visvikis D, Wahid K, Zaidi H, Hatt M, Depeursinge A. Overview of the HECKTOR Challenge at MICCAI 2022: Automatic Head and Neck Tumor Segmentation and Outcome Prediction in PET/CT. Head Neck Tumor Chall (2022) 2023; 13626:1-30. [PMID: 37195050 PMCID: PMC10171217 DOI: 10.1007/978-3-031-27420-6_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This paper presents an overview of the third edition of the HEad and neCK TumOR segmentation and outcome prediction (HECKTOR) challenge, organized as a satellite event of the 25th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2022. The challenge comprises two tasks related to the automatic analysis of FDG-PET/CT images for patients with Head and Neck cancer (H&N), focusing on the oropharynx region. Task 1 is the fully automatic segmentation of H&N primary Gross Tumor Volume (GTVp) and metastatic lymph nodes (GTVn) from FDG-PET/CT images. Task 2 is the fully automatic prediction of Recurrence-Free Survival (RFS) from the same FDG-PET/CT and clinical data. The data were collected from nine centers for a total of 883 cases consisting of FDG-PET/CT images and clinical information, split into 524 training and 359 test cases. The best methods obtained an aggregated Dice Similarity Coefficient (DSCagg) of 0.788 in Task 1, and a Concordance index (C-index) of 0.682 in Task 2.
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Affiliation(s)
- Vincent Andrearczyk
- Institute of Informatics, HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland, Sierre, Switzerland
| | - Valentin Oreiller
- Institute of Informatics, HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland, Sierre, Switzerland
- Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011 Lausanne, Switzerland
| | - Moamen Abobakr
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | | | | | - Sarah Boughdad
- Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011 Lausanne, Switzerland
| | - Leo Capriotti
- Center Henri Becquerel, LITIS Laboratory, University of Rouen Normandy, Rouen, France
| | - Joel Castelli
- Radiotherapy Department, Cancer Institute Eugène Marquis, Rennes, France
- INSERM, U1099, Rennes, France
- University of Rennes 1, LTSI, Rennes, France
| | - Catherine Cheze Le Rest
- Centre Hospitalier Universitaire de Poitiers (CHUP), Poitiers, France
- LaTIM, INSERM, UMR 1101, Univ Brest, Brest, France
| | - Pierre Decazes
- Center Henri Becquerel, LITIS Laboratory, University of Rouen Normandy, Rouen, France
| | - Ricardo Correia
- Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011 Lausanne, Switzerland
| | - Dina El-Habashy
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Hesham Elhalawani
- Cleveland Clinic Foundation, Department of Radiation Oncology, Cleveland, OH, USA
| | | | - Mario Jreige
- Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011 Lausanne, Switzerland
| | - Yornna Khamis
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | | | | | - Mohamed Naser
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - John O Prior
- Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011 Lausanne, Switzerland
| | - Su Ruan
- Center Henri Becquerel, LITIS Laboratory, University of Rouen Normandy, Rouen, France
| | | | - Olena Tankyevych
- Centre Hospitalier Universitaire de Poitiers (CHUP), Poitiers, France
- LaTIM, INSERM, UMR 1101, Univ Brest, Brest, France
| | | | - Martin Vallières
- Department of Computer Science, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre Vera
- Center Henri Becquerel, LITIS Laboratory, University of Rouen Normandy, Rouen, France
| | | | - Kareem Wahid
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Habib Zaidi
- Geneva University Hospital, Geneva, Switzerland
| | - Mathieu Hatt
- LaTIM, INSERM, UMR 1101, Univ Brest, Brest, France
| | - Adrien Depeursinge
- Institute of Informatics, HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland, Sierre, Switzerland
- Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011 Lausanne, Switzerland
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Hajianfar G, Sabouri M, Salimi Y, Amini M, Bagheri S, Jenabi E, Hekmat S, Maghsudi M, Mansouri Z, Khateri M, Hosein Jamshidi M, Jafari E, Bitarafan Rajabi A, Assadi M, Oveisi M, Shiri I, Zaidi H. Artificial intelligence-based analysis of whole-body bone scintigraphy: The quest for the optimal deep learning algorithm and comparison with human observer performance. Z Med Phys 2023:S0939-3889(23)00008-9. [PMID: 36932023 DOI: 10.1016/j.zemedi.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/22/2022] [Accepted: 01/18/2023] [Indexed: 03/17/2023]
Abstract
PURPOSE Whole-body bone scintigraphy (WBS) is one of the most widely used modalities in diagnosing malignant bone diseases during the early stages. However, the procedure is time-consuming and requires vigour and experience. Moreover, interpretation of WBS scans in the early stages of the disorders might be challenging because the patterns often reflect normal appearance that is prone to subjective interpretation. To simplify the gruelling, subjective, and prone-to-error task of interpreting WBS scans, we developed deep learning (DL) models to automate two major analyses, namely (i) classification of scans into normal and abnormal and (ii) discrimination between malignant and non-neoplastic bone diseases, and compared their performance with human observers. MATERIALS AND METHODS After applying our exclusion criteria on 7188 patients from three different centers, 3772 and 2248 patients were enrolled for the first and second analyses, respectively. Data were split into two parts, including training and testing, while a fraction of training data were considered for validation. Ten different CNN models were applied to single- and dual-view input (posterior and anterior views) modes to find the optimal model for each analysis. In addition, three different methods, including squeeze-and-excitation (SE), spatial pyramid pooling (SPP), and attention-augmented (AA), were used to aggregate the features for dual-view input models. Model performance was reported through area under the receiver operating characteristic (ROC) curve (AUC), accuracy, sensitivity, and specificity and was compared with the DeLong test applied to ROC curves. The test dataset was evaluated by three nuclear medicine physicians (NMPs) with different levels of experience to compare the performance of AI and human observers. RESULTS DenseNet121_AA (DensNet121, with dual-view input aggregated by AA) and InceptionResNetV2_SPP achieved the highest performance (AUC = 0.72) for the first and second analyses, respectively. Moreover, on average, in the first analysis, Inception V3 and InceptionResNetV2 CNN models and dual-view input with AA aggregating method had superior performance. In addition, in the second analysis, DenseNet121 and InceptionResNetV2 as CNN methods and dual-view input with AA aggregating method achieved the best results. Conversely, the performance of AI models was significantly higher than human observers for the first analysis, whereas their performance was comparable in the second analysis, although the AI model assessed the scans in a drastically lower time. CONCLUSION Using the models designed in this study, a positive step can be taken toward improving and optimizing WBS interpretation. By training DL models with larger and more diverse cohorts, AI could potentially be used to assist physicians in the assessment of WBS images.
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Affiliation(s)
- Ghasem Hajianfar
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva 4, Switzerland
| | - Maziar Sabouri
- Department of Medical Physics, School of Medicine, Iran University of Medical Science, Tehran, Iran; Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva 4, Switzerland
| | - Mehdi Amini
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva 4, Switzerland
| | - Soroush Bagheri
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Elnaz Jenabi
- Research Center for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Hekmat
- Hasheminejad Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Maghsudi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Mansouri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva 4, Switzerland
| | - Maziar Khateri
- Department of Medical Radiation Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Hosein Jamshidi
- Department of Medical Imaging and Radiation Sciences, School of Allied Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Esmail Jafari
- The Persian Gulf Nuclear Medicine Research Center, Department of Molecular Imaging and Radionuclide Therapy, Bushehr Medical University Hospital, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Ahmad Bitarafan Rajabi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Assadi
- The Persian Gulf Nuclear Medicine Research Center, Department of Molecular Imaging and Radionuclide Therapy, Bushehr Medical University Hospital, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mehrdad Oveisi
- Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
| | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva 4, Switzerland
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva 4, Switzerland; Geneva University Neurocenter, Geneva University, Geneva, Switzerland; Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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18
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Shiri I, Vafaei Sadr A, Akhavan A, Salimi Y, Sanaat A, Amini M, Razeghi B, Saberi A, Arabi H, Ferdowsi S, Voloshynovskiy S, Gündüz D, Rahmim A, Zaidi H. Decentralized collaborative multi-institutional PET attenuation and scatter correction using federated deep learning. Eur J Nucl Med Mol Imaging 2023; 50:1034-1050. [PMID: 36508026 PMCID: PMC9742659 DOI: 10.1007/s00259-022-06053-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
PURPOSE Attenuation correction and scatter compensation (AC/SC) are two main steps toward quantitative PET imaging, which remain challenging in PET-only and PET/MRI systems. These can be effectively tackled via deep learning (DL) methods. However, trustworthy, and generalizable DL models commonly require well-curated, heterogeneous, and large datasets from multiple clinical centers. At the same time, owing to legal/ethical issues and privacy concerns, forming a large collective, centralized dataset poses significant challenges. In this work, we aimed to develop a DL-based model in a multicenter setting without direct sharing of data using federated learning (FL) for AC/SC of PET images. METHODS Non-attenuation/scatter corrected and CT-based attenuation/scatter corrected (CT-ASC) 18F-FDG PET images of 300 patients were enrolled in this study. The dataset consisted of 6 different centers, each with 50 patients, with scanner, image acquisition, and reconstruction protocols varying across the centers. CT-based ASC PET images served as the standard reference. All images were reviewed to include high-quality and artifact-free PET images. Both corrected and uncorrected PET images were converted to standardized uptake values (SUVs). We used a modified nested U-Net utilizing residual U-block in a U-shape architecture. We evaluated two FL models, namely sequential (FL-SQ) and parallel (FL-PL) and compared their performance with the baseline centralized (CZ) learning model wherein the data were pooled to one server, as well as center-based (CB) models where for each center the model was built and evaluated separately. Data from each center were divided to contribute to training (30 patients), validation (10 patients), and test sets (10 patients). Final evaluations and reports were performed on 60 patients (10 patients from each center). RESULTS In terms of percent SUV absolute relative error (ARE%), both FL-SQ (CI:12.21-14.81%) and FL-PL (CI:11.82-13.84%) models demonstrated excellent agreement with the centralized framework (CI:10.32-12.00%), while FL-based algorithms improved model performance by over 11% compared to CB training strategy (CI: 22.34-26.10%). Furthermore, the Mann-Whitney test between different strategies revealed no significant differences between CZ and FL-based algorithms (p-value > 0.05) in center-categorized mode. At the same time, a significant difference was observed between the different training approaches on the overall dataset (p-value < 0.05). In addition, voxel-wise comparison, with respect to reference CT-ASC, exhibited similar performance for images predicted by CZ (R2 = 0.94), FL-SQ (R2 = 0.93), and FL-PL (R2 = 0.92), while CB model achieved a far lower coefficient of determination (R2 = 0.74). Despite the strong correlations between CZ and FL-based methods compared to reference CT-ASC, a slight underestimation of predicted voxel values was observed. CONCLUSION Deep learning-based models provide promising results toward quantitative PET image reconstruction. Specifically, we developed two FL models and compared their performance with center-based and centralized models. The proposed FL-based models achieved higher performance compared to center-based models, comparable with centralized models. Our work provided strong empirical evidence that the FL framework can fully benefit from the generalizability and robustness of DL models used for AC/SC in PET, while obviating the need for the direct sharing of datasets between clinical imaging centers.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Alireza Vafaei Sadr
- Department of Theoretical Physics and Center for Astroparticle Physics, University of Geneva, Geneva, Switzerland.,Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Azadeh Akhavan
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Amirhossein Sanaat
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Mehdi Amini
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Behrooz Razeghi
- Department of Computer Science, University of Geneva, Geneva, Switzerland
| | - Abdollah Saberi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | | | | | - Deniz Gündüz
- Department of Electrical and Electronic Engineering, Imperial College London, London, UK
| | - Arman Rahmim
- Departments of Radiology and Physics, University of British Columbia, Vancouver, Canada.,Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland. .,Geneva University Neurocenter, Geneva University, Geneva, Switzerland. .,Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands. .,Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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Jamshidi MH, Karami A, Salimi Y, Keshavarz A. Patient effective dose and radiation biological risk in the chest and abdominopelvic computed tomography. Appl Radiat Isot 2023; 193:110628. [PMID: 36577360 DOI: 10.1016/j.apradiso.2022.110628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/03/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
The incidence and mortality (per 100,000) rates in chest CT are highest for the lungs and breasts (incidence: lung = 116, breast = 98.64; mortality: lung = 113.43, breast = 49.72). Abdominopelvic CT scans showed the highest incidence for stomach (79.57), colon (62.86), bladder (48.69), and liver (28.63), respectively. Mortality is highest for the bladder (80.44), stomach (72.43), colon (69.02), and liver (63.78), respectively. This study helps to better understand the concept of radiation dose and the numbers reported as organ dose and effective dose and identify the probability of the stochastic effect.
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Affiliation(s)
- Mohammad Hossein Jamshidi
- Department of Medical Imaging and Radiation Sciences, School of Allied Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Aida Karami
- Department of Medical Imaging and Radiation Sciences, School of Allied Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Yazdan Salimi
- Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhesam Keshavarz
- Department of Anatomical Science, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Salimi Y, Shiri I, Akavanallaf A, Mansouri Z, Arabi H, Zaidi H. Fully automated accurate patient positioning in computed tomography using anterior-posterior localizer images and a deep neural network: a dual-center study. Eur Radiol 2023; 33:3243-3252. [PMID: 36703015 PMCID: PMC9879741 DOI: 10.1007/s00330-023-09424-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 11/29/2022] [Accepted: 01/02/2023] [Indexed: 01/28/2023]
Abstract
OBJECTIVES This study aimed to improve patient positioning accuracy by relying on a CT localizer and a deep neural network to optimize image quality and radiation dose. METHODS We included 5754 chest CT axial and anterior-posterior (AP) images from two different centers, C1 and C2. After pre-processing, images were split into training (80%) and test (20%) datasets. A deep neural network was trained to generate 3D axial images from the AP localizer. The geometric centerlines of patient bodies were indicated by creating a bounding box on the predicted images. The distance between the body centerline, estimated by the deep learning model and ground truth (BCAP), was compared with patient mis-centering during manual positioning (BCMP). We evaluated the performance of our model in terms of distance between the lung centerline estimated by the deep learning model and the ground truth (LCAP). RESULTS The error in terms of BCAP was - 0.75 ± 7.73 mm and 2.06 ± 10.61 mm for C1 and C2, respectively. This error was significantly lower than BCMP, which achieved an error of 9.35 ± 14.94 and 13.98 ± 14.5 mm for C1 and C2, respectively. The absolute BCAP was 5.7 ± 5.26 and 8.26 ± 6.96 mm for C1 and C2, respectively. The LCAP metric was 1.56 ± 10.8 and -0.27 ± 16.29 mm for C1 and C2, respectively. The error in terms of BCAP and LCAP was higher for larger patients (p value < 0.01). CONCLUSION The accuracy of the proposed method was comparable to available alternative methods, carrying the advantage of being free from errors related to objects blocking the camera visibility. KEY POINTS • Patient mis-centering in the anterior-posterior direction (AP) is a common problem in clinical practice which can degrade image quality and increase patient radiation dose. • We proposed a deep neural network for automatic patient positioning using only the CT image localizer, achieving a performance comparable to alternative techniques, such as the external 3D visual camera. • The advantage of the proposed method is that it is free from errors related to objects blocking the camera visibility and that it could be implemented on imaging consoles as a patient positioning support tool.
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Affiliation(s)
- Yazdan Salimi
- grid.150338.c0000 0001 0721 9812Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland
| | - Isaac Shiri
- grid.150338.c0000 0001 0721 9812Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland
| | - Azadeh Akavanallaf
- grid.150338.c0000 0001 0721 9812Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland
| | - Zahra Mansouri
- grid.150338.c0000 0001 0721 9812Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland
| | - Hossein Arabi
- grid.150338.c0000 0001 0721 9812Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland
| | - Habib Zaidi
- grid.150338.c0000 0001 0721 9812Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Geneva University Neurocenter, Geneva University, Geneva, Switzerland ,grid.4494.d0000 0000 9558 4598Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands ,grid.10825.3e0000 0001 0728 0170Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark
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Salimi Y, Shiri I, Akhavanallaf A, Mansouri Z, Sanaat A, Pakbin M, Ghasemian M, Arabi H, Zaidi H. Deep Learning-based Calculation of Patient Size and Attenuation Surrogates from Localizer Image: Toward Personalized Chest CT Protocol Optimization. Eur J Radiol 2022; 157:110602. [DOI: 10.1016/j.ejrad.2022.110602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
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22
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Sanaat A, Akhavanalaf A, Shiri I, Salimi Y, Arabi H, Zaidi H. Deep-TOF-PET: Deep learning-guided generation of time-of-flight from non-TOF brain PET images in the image and projection domains. Hum Brain Mapp 2022; 43:5032-5043. [PMID: 36087092 PMCID: PMC9582376 DOI: 10.1002/hbm.26068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/18/2022] [Indexed: 11/12/2022] Open
Abstract
We aim to synthesize brain time‐of‐flight (TOF) PET images/sinograms from their corresponding non‐TOF information in the image space (IS) and sinogram space (SS) to increase the signal‐to‐noise ratio (SNR) and contrast of abnormalities, and decrease the bias in tracer uptake quantification. One hundred forty clinical brain 18F‐FDG PET/CT scans were collected to generate TOF and non‐TOF sinograms. The TOF sinograms were split into seven time bins (0, ±1, ±2, ±3). The predicted TOF sinogram was reconstructed and the performance of both models (IS and SS) compared with reference TOF and non‐TOF. Wide‐ranging quantitative and statistical analysis metrics, including structural similarity index metric (SSIM), root mean square error (RMSE), as well as 28 radiomic features for 83 brain regions were extracted to evaluate the performance of the CycleGAN model. SSIM and RMSE of 0.99 ± 0.03, 0.98 ± 0.02 and 0.12 ± 0.09, 0.16 ± 0.04 were achieved for the generated TOF‐PET images in IS and SS, respectively. They were 0.97 ± 0.03 and 0.22 ± 0.12, respectively, for non‐TOF‐PET images. The Bland & Altman analysis revealed that the lowest tracer uptake value bias (−0.02%) and minimum variance (95% CI: −0.17%, +0.21%) were achieved for TOF‐PET images generated in IS. For malignant lesions, the contrast in the test dataset was enhanced from 3.22 ± 2.51 for non‐TOF to 3.34 ± 0.41 and 3.65 ± 3.10 for TOF PET in SS and IS, respectively. The implemented CycleGAN is capable of generating TOF from non‐TOF PET images to achieve better image quality.
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Affiliation(s)
- Amirhossein Sanaat
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Azadeh Akhavanalaf
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland.,Geneva University Neurocenter, Geneva University, Geneva, Switzerland.,Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark
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23
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Shiri I, Mostafaei S, Haddadi Avval A, Salimi Y, Sanaat A, Akhavanallaf A, Arabi H, Rahmim A, Zaidi H. High-dimensional multinomial multiclass severity scoring of COVID-19 pneumonia using CT radiomics features and machine learning algorithms. Sci Rep 2022; 12:14817. [PMID: 36050434 PMCID: PMC9437017 DOI: 10.1038/s41598-022-18994-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/23/2022] [Indexed: 12/11/2022] Open
Abstract
We aimed to construct a prediction model based on computed tomography (CT) radiomics features to classify COVID-19 patients into severe-, moderate-, mild-, and non-pneumonic. A total of 1110 patients were studied from a publicly available dataset with 4-class severity scoring performed by a radiologist (based on CT images and clinical features). The entire lungs were segmented and followed by resizing, bin discretization and radiomic features extraction. We utilized two feature selection algorithms, namely bagging random forest (BRF) and multivariate adaptive regression splines (MARS), each coupled to a classifier, namely multinomial logistic regression (MLR), to construct multiclass classification models. The dataset was divided into 50% (555 samples), 20% (223 samples), and 30% (332 samples) for training, validation, and untouched test datasets, respectively. Subsequently, nested cross-validation was performed on train/validation to select the features and tune the models. All predictive power indices were reported based on the testing set. The performance of multi-class models was assessed using precision, recall, F1-score, and accuracy based on the 4 × 4 confusion matrices. In addition, the areas under the receiver operating characteristic curves (AUCs) for multi-class classifications were calculated and compared for both models. Using BRF, 23 radiomic features were selected, 11 from first-order, 9 from GLCM, 1 GLRLM, 1 from GLDM, and 1 from shape. Ten features were selected using the MARS algorithm, namely 3 from first-order, 1 from GLDM, 1 from GLRLM, 1 from GLSZM, 1 from shape, and 3 from GLCM features. The mean absolute deviation, skewness, and variance from first-order and flatness from shape, and cluster prominence from GLCM features and Gray Level Non Uniformity Normalize from GLRLM were selected by both BRF and MARS algorithms. All selected features by BRF or MARS were significantly associated with four-class outcomes as assessed within MLR (All p values < 0.05). BRF + MLR and MARS + MLR resulted in pseudo-R2 prediction performances of 0.305 and 0.253, respectively. Meanwhile, there was a significant difference between the feature selection models when using a likelihood ratio test (p value = 0.046). Based on confusion matrices for BRF + MLR and MARS + MLR algorithms, the precision was 0.856 and 0.728, the recall was 0.852 and 0.722, whereas the accuracy was 0.921 and 0.861, respectively. AUCs (95% CI) for multi-class classification were 0.846 (0.805-0.887) and 0.807 (0.752-0.861) for BRF + MLR and MARS + MLR algorithms, respectively. Our models based on the utilization of radiomic features, coupled with machine learning were able to accurately classify patients according to the severity of pneumonia, thus highlighting the potential of this emerging paradigm in the prognostication and management of COVID-19 patients.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Shayan Mostafaei
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | | | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Amirhossein Sanaat
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Arman Rahmim
- Departments of Radiology and Physics, University of British Columbia, Vancouver, BC, Canada.,Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland. .,Geneva University Neurocenter, Geneva University, Geneva, Switzerland. .,Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. .,Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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Deevband MR, Hosseini Nasab SMB, Mohammadi H, Salimi Y, Mostaar A, Deravi N, Fathi M, Vakili K, Yaghoobpoor S, Ghorbani M. Body-Mass Index-Based Effective Dose Determination in Commonly Performed Computed Tomography Examinations in Adults. fbt 2022. [DOI: 10.18502/fbt.v9i4.10425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose: With the widespread application of ionizing radiation in medical practice, concerns have been increased regarding the hazardous effects of radiation. Studies have demonstrated that some variables such as body dimensions affect the absorbed radiation dose. In this study, the association between Body Mass Index (BMI) and absorbed dose in Computed Tomography (CT) is investigated.
Materials and Methods: A total of 550 adult patients (age ≥ 15 years) were included in the study. The height and weight of the patients were recorded for BMI calculation. Dosimetry data were acquired from digital imaging and communications in medicine dose reports. The patients were categorized into five groups according to their BMI, the categorized information was then imported into ImPACT Dose software for calculation of Size-Specific Dose Estimate (SSDE) and organ and effective doses. The relationship between patient BMI and the effective dose was also determined.
Results: A higher BMI contributed to increased radiation dose and SSDE in patients who had undergone chest or abdomen-pelvis CT examination (p < 0.05).
Conclusion: The radiation dose is related to a patient’s BMI and rises with an increase in BMI. Accordingly, it is suggested that BMI and other variables, such as the type of scan and other body dimensions, which affect the radiation dose, can be used to estimate the radiation dose before performing CT. This estimation can be considered for the justification and optimization of CT examinations.
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Norouzi G, AsadZade A, Salimi Y, Khoshbakht S, Pirayesh E. Effect of proton pump inhibitors and H2 antagonists on gastric wall uptake in myocardial perfusion scan with 99mTc-sestamibi. J Nucl Cardiol 2022; 29:1552-1561. [PMID: 33527332 DOI: 10.1007/s12350-021-02529-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/14/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Proton pump inhibitors (PPIs) have been speculated to cause gastric wall uptake (GWU) in MPI scans. However, the uptake mechanism and prevention methods are less studied. In this prospective trial we aimed to evaluate the impact of gastroprotective medications on GWU and its solutions. METHODS 351 consecutive patients, scheduled for 2-day rest/stress 99mTc-MIBI scan, were distributed into 5 groups. 3-7 days following the baseline rest scan, the stress scan was acquired after intervention in the trial group, consisting of patients with history of PPI intake, randomly assigned to 3 subgroups: discontinuing PPIs(A), replacement with H2 blockers (B), and continuing PPIs (C). Patients receiving H2 blockers, continued it as before (D) and the remaining patients were the control group (E). GWU was graded compared to the myocardial uptake. RESULTS In the rest phase, all groups had significantly higher GWU compared to the control group. In the stress phase, group A had less GWU than group B (P-value < 0.05) and both of them had significantly less GWU compared to group C (P-value < 0.001). There was no significant difference between PPI discontinuation periods of 3-5 days versus 5-7 days. There was a significant association between duration of oral PPI intake, but not IV PPIs, and GWU. GWU was significantly lower with oral compared to IV PPI administration. CONCLUSION PPIs significantly increase GWU and discontinuing them for at least 3-5 days significantly reduces GWU. H2 antagonists are a good alternative in patients who cannot tolerate dyspepsia symptoms.
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Affiliation(s)
- Ghazal Norouzi
- Department of Nuclear Medicine, Shohadae Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, TajrishSq, Tehran, Iran
- Clinical Research Development Unit of Shohadae Tajrish Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azin AsadZade
- Department of Nuclear Medicine, Shohadae Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, TajrishSq, Tehran, Iran
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Sepide Khoshbakht
- Department of Nuclear Medicine, Shohadae Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, TajrishSq, Tehran, Iran
- Clinical Research Development Unit of Shohadae Tajrish Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elahe Pirayesh
- Department of Nuclear Medicine, Shohadae Tajrish Medical Center, School of Medicine, Shahid Beheshti University of Medical Sciences, TajrishSq, Tehran, Iran.
- Clinical Research Development Unit of Shohadae Tajrish Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Falahatpour Z, Geramifar P, Mahdavi SR, Abdollahi H, Salimi Y, Nikoofar A, Ay MR. Potential advantages of FDG-PET radiomic feature map for target volume delineation in lung cancer radiotherapy. J Appl Clin Med Phys 2022; 23:e13696. [PMID: 35699200 PMCID: PMC9512354 DOI: 10.1002/acm2.13696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 04/20/2022] [Accepted: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To investigate the potential benefits of FDG PET radiomic feature maps (RFMs) for target delineation in non-small cell lung cancer (NSCLC) radiotherapy. METHODS Thirty-two NSCLC patients undergoing FDG PET/CT imaging were included. For each patient, nine grey-level co-occurrence matrix (GLCM) RFMs were generated. gross target volume (GTV) and clinical target volume (CTV) were contoured on CT (GTVCT , CTVCT ), PET (GTVPET40 , CTVPET40 ), and RFMs (GTVRFM , CTVRFM ,). Intratumoral heterogeneity areas were segmented as GTVPET50-Boost and radiomic boost target volume (RTVBoost ) on PET and RFMs, respectively. GTVCT in homogenous tumors and GTVPET40 in heterogeneous tumors were considered as GTVgold standard (GTVGS ). One-way analysis of variance was conducted to determine the threshold that finds the best conformity for GTVRFM with GTVGS . Dice similarity coefficient (DSC) and mean absolute percent error (MAPE) were calculated. Linear regression analysis was employed to report the correlations between the gold standard and RFM-derived target volumes. RESULTS Entropy, contrast, and Haralick correlation (H-correlation) were selected for tumor segmentation. The threshold values of 80%, 50%, and 10% have the best conformity of GTVRFM-entropy , GTVRFM-contrast , and GTVRFM-H-correlation with GTVGS , respectively. The linear regression results showed a positive correlation between GTVGS and GTVRFM-entropy (r = 0.98, p < 0.001), between GTVGS and GTVRFM-contrast (r = 0.93, p < 0.001), and between GTVGS and GTVRFM-H-correlation (r = 0.91, p < 0.001). The average threshold values of 45% and 15% were resulted in the best segmentation matching between CTVRFM-entropy and CTVRFM-contrast with CTVGS , respectively. Moreover, we used RFM to determine RTVBoost in the heterogeneous tumors. Comparison of RTVBoost with GTVPET50-Boost MAPE showed the volume error differences of 31.7%, 36%, and 34.7% in RTVBoost-entropy , RTVBoost-contrast , and RTVBoost-H-correlation , respectively. CONCLUSIONS FDG PET-based radiomics features in NSCLC demonstrated a promising potential for decision support in radiotherapy, helping radiation oncologists delineate tumors and generate accurate segmentation for heterogeneous region of tumors.
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Affiliation(s)
- Zahra Falahatpour
- Department of Medical Physics, Tehran University of Medical Sciences, Tehran, Iran
| | - Parham Geramifar
- Research Center for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Rabie Mahdavi
- Department of Medical Physics, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Abdollahi
- Department of Radiology Technology, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Yazdan Salimi
- Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Nikoofar
- Department of Radiation Oncology, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Ay
- Department of Medical Physics, Tehran University of Medical Sciences, Tehran, Iran
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Shiri I, Salimi Y, Pakbin M, Hajianfar G, Avval AH, Sanaat A, Mostafaei S, Akhavanallaf A, Saberi A, Mansouri Z, Askari D, Ghasemian M, Sharifipour E, Sandoughdaran S, Sohrabi A, Sadati E, Livani S, Iranpour P, Kolahi S, Khateri M, Bijari S, Atashzar MR, Shayesteh SP, Khosravi B, Babaei MR, Jenabi E, Hasanian M, Shahhamzeh A, Foroghi Ghomi SY, Mozafari A, Teimouri A, Movaseghi F, Ahmari A, Goharpey N, Bozorgmehr R, Shirzad-Aski H, Mortazavi R, Karimi J, Mortazavi N, Besharat S, Afsharpad M, Abdollahi H, Geramifar P, Radmard AR, Arabi H, Rezaei-Kalantari K, Oveisi M, Rahmim A, Zaidi H. COVID-19 prognostic modeling using CT radiomic features and machine learning algorithms: Analysis of a multi-institutional dataset of 14,339 patients. Comput Biol Med 2022; 145:105467. [PMID: 35378436 PMCID: PMC8964015 DOI: 10.1016/j.compbiomed.2022.105467] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/24/2022] [Accepted: 03/26/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND We aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients. METHODS Whole lung segmentations were performed automatically using a deep learning-based model to extract 107 intensity and texture radiomics features. We used four feature selection algorithms and seven classifiers. We evaluated the models using ten different splitting and cross-validation strategies, including non-harmonized and ComBat-harmonized datasets. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were reported. RESULTS In the test dataset (4,301) consisting of CT and/or RT-PCR positive cases, AUC, sensitivity, and specificity of 0.83 ± 0.01 (CI95%: 0.81-0.85), 0.81, and 0.72, respectively, were obtained by ANOVA feature selector + Random Forest (RF) classifier. Similar results were achieved in RT-PCR-only positive test sets (3,644). In ComBat harmonized dataset, Relief feature selector + RF classifier resulted in the highest performance of AUC, reaching 0.83 ± 0.01 (CI95%: 0.81-0.85), with a sensitivity and specificity of 0.77 and 0.74, respectively. ComBat harmonization did not depict statistically significant improvement compared to a non-harmonized dataset. In leave-one-center-out, the combination of ANOVA feature selector and RF classifier resulted in the highest performance. CONCLUSION Lung CT radiomics features can be used for robust prognostic modeling of COVID-19. The predictive power of the proposed CT radiomics model is more reliable when using a large multicentric heterogeneous dataset, and may be used prospectively in clinical setting to manage COVID-19 patients.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, 1211, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, 1211, Switzerland
| | - Masoumeh Pakbin
- Imaging Department, Qom University of Medical Sciences, Qum, Iran
| | - Ghasem Hajianfar
- Rajaie Cardiovascular, Medical & Research Center, Iran University of Medical Science, Tehran, Iran
| | | | - Amirhossein Sanaat
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, 1211, Switzerland
| | - Shayan Mostafaei
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, 1211, Switzerland
| | - Abdollah Saberi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, 1211, Switzerland
| | - Zahra Mansouri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, 1211, Switzerland
| | - Dariush Askari
- Department of Radiology Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Ghasemian
- Department of Radiology, Shahid Beheshti Hospital, Qom University of Medical Sciences, Qum, Iran
| | - Ehsan Sharifipour
- Neuroscience Research Center, Qom University of Medical Sciences, Qum, Iran
| | - Saleh Sandoughdaran
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmad Sohrabi
- Cancer Control Research Center, Cancer Control Foundation, Iran University of Medical Sciences, Tehran, Iran
| | - Elham Sadati
- Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Somayeh Livani
- Clinical Research Development Unit (CRDU), Sayad Shirazi Hospital, Golestan University of Medical Sciences, Gorgan, Iran
| | - Pooya Iranpour
- Medical Imaging Research Center, Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shahriar Kolahi
- Department of Radiology, School of Medicine, Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Maziar Khateri
- Department of Medical Radiation Engineering, Science and Research Branch, Islamic Azad University, Tehran, Tehran, Iran
| | - Salar Bijari
- Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Reza Atashzar
- Department of Immunology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Sajad P. Shayesteh
- Department of Physiology, Pharmacology and Medical Physics, Alborz University of Medical Sciences, Karaj, Iran
| | - Bardia Khosravi
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Babaei
- Department of Interventional Radiology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Elnaz Jenabi
- Research Centre for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hasanian
- Department of Radiology, Arak University of Medical Sciences, Arak, Iran
| | - Alireza Shahhamzeh
- Clinical Research Development Center, Qom University of Medical Sciences, Qum, Iran
| | - Seyaed Yaser Foroghi Ghomi
- Clinical Research Development Center, Shahid Beheshti Hospital, Qom University Of Medical Sciences, Qom, Iran
| | - Abolfazl Mozafari
- Department of Medical Sciences, Qom Branch, Islamic Azad University, Qum, Iran
| | - Arash Teimouri
- Medical Imaging Research Center, Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Movaseghi
- Department of Medical Sciences, Qom Branch, Islamic Azad University, Qum, Iran
| | - Azin Ahmari
- Ayatolah Khansary Hospital, Arak University of Medical Sciences, Arak, Iran
| | - Neda Goharpey
- Department of Radiation Oncology, Shohadaye Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rama Bozorgmehr
- Clinical Research Development Unit, Shohadaye Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Roozbeh Mortazavi
- Department of Internal Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jalal Karimi
- Department of Infectious Disease, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Nazanin Mortazavi
- Dental Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Sima Besharat
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mandana Afsharpad
- Cancer Control Research Center, Cancer Control Foundation, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Abdollahi
- Department of Radiologic Technology, Faculty of Allied Medical Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Parham Geramifar
- Research Centre for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Reza Radmard
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, 1211, Switzerland
| | - Kiara Rezaei-Kalantari
- Rajaie Cardiovascular, Medical & Research Center, Iran University of Medical Science, Tehran, Iran
| | - Mehrdad Oveisi
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
| | - Arman Rahmim
- Departments of Radiology and Physics, University of British Columbia, Vancouver, BC, Canada,Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, 1211, Switzerland,Geneva University Neurocenter, Geneva University, Geneva, Switzerland,Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands,Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark,Corresponding author. Geneva University Hospital Division of Nuclear Medicine and Molecular Imaging, CH-1211, Geneva, Switzerland
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Akhavanallaf A, Fayad H, Salimi Y, Aly A, Kharita H, Al Naemi H, Zaidi H. An update on computational anthropomorphic anatomical models. Digit Health 2022; 8:20552076221111941. [PMID: 35847523 PMCID: PMC9277432 DOI: 10.1177/20552076221111941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/19/2022] [Indexed: 11/15/2022] Open
Abstract
The prevalent availability of high-performance computing coupled with validated
computerized simulation platforms as open-source packages have motivated
progress in the development of realistic anthropomorphic computational models of
the human anatomy. The main application of these advanced tools focused on
imaging physics and computational internal/external radiation dosimetry
research. This paper provides an updated review of state-of-the-art developments
and recent advances in the design of sophisticated computational models of the
human anatomy with a particular focus on their use in radiation dosimetry
calculations. The consolidation of flexible and realistic computational models
with biological data and accurate radiation transport modeling tools enables the
capability to produce dosimetric data reflecting actual setup in clinical
setting. These simulation methodologies and results are helpful resources for
the medical physics and medical imaging communities and are expected to impact
the fields of medical imaging and dosimetry calculations profoundly.
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Affiliation(s)
- Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Hadi Fayad
- Hamad Medical Corporation, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Antar Aly
- Hamad Medical Corporation, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | | | - Huda Al Naemi
- Hamad Medical Corporation, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
- Geneva University Neurocenter, Geneva University, Geneva, Switzerland
- Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark
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Shiri I, Arabi H, Salimi Y, Sanaat A, Akhavanallaf A, Hajianfar G, Askari D, Moradi S, Mansouri Z, Pakbin M, Sandoughdaran S, Abdollahi H, Radmard AR, Rezaei‐Kalantari K, Ghelich Oghli M, Zaidi H. COLI-Net: Deep learning-assisted fully automated COVID-19 lung and infection pneumonia lesion detection and segmentation from chest computed tomography images. Int J Imaging Syst Technol 2022; 32:12-25. [PMID: 34898850 PMCID: PMC8652855 DOI: 10.1002/ima.22672] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/18/2021] [Accepted: 10/17/2021] [Indexed: 05/17/2023]
Abstract
We present a deep learning (DL)-based automated whole lung and COVID-19 pneumonia infectious lesions (COLI-Net) detection and segmentation from chest computed tomography (CT) images. This multicenter/multiscanner study involved 2368 (347'259 2D slices) and 190 (17 341 2D slices) volumetric CT exams along with their corresponding manual segmentation of lungs and lesions, respectively. All images were cropped, resized, and the intensity values clipped and normalized. A residual network with non-square Dice loss function built upon TensorFlow was employed. The accuracy of lung and COVID-19 lesions segmentation was evaluated on an external reverse transcription-polymerase chain reaction positive COVID-19 dataset (7'333 2D slices) collected at five different centers. To evaluate the segmentation performance, we calculated different quantitative metrics, including radiomic features. The mean Dice coefficients were 0.98 ± 0.011 (95% CI, 0.98-0.99) and 0.91 ± 0.038 (95% CI, 0.90-0.91) for lung and lesions segmentation, respectively. The mean relative Hounsfield unit differences were 0.03 ± 0.84% (95% CI, -0.12 to 0.18) and -0.18 ± 3.4% (95% CI, -0.8 to 0.44) for the lung and lesions, respectively. The relative volume difference for lung and lesions were 0.38 ± 1.2% (95% CI, 0.16-0.59) and 0.81 ± 6.6% (95% CI, -0.39 to 2), respectively. Most radiomic features had a mean relative error less than 5% with the highest mean relative error achieved for the lung for the range first-order feature (-6.95%) and least axis length shape feature (8.68%) for lesions. We developed an automated DL-guided three-dimensional whole lung and infected regions segmentation in COVID-19 patients to provide fast, consistent, robust, and human error immune framework for lung and pneumonia lesion detection and quantification.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular ImagingGeneva University HospitalGenevaSwitzerland
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular ImagingGeneva University HospitalGenevaSwitzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular ImagingGeneva University HospitalGenevaSwitzerland
| | - Amirhossein Sanaat
- Division of Nuclear Medicine and Molecular ImagingGeneva University HospitalGenevaSwitzerland
| | - Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular ImagingGeneva University HospitalGenevaSwitzerland
| | - Ghasem Hajianfar
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Dariush Askari
- Department of Radiology TechnologyShahid Beheshti University of Medical SciencesTehranIran
| | - Shakiba Moradi
- Research and Development DepartmentMed Fanavaran Plus Co.KarajIran
| | - Zahra Mansouri
- Division of Nuclear Medicine and Molecular ImagingGeneva University HospitalGenevaSwitzerland
| | - Masoumeh Pakbin
- Clinical Research Development CenterQom University of Medical SciencesQomIran
| | - Saleh Sandoughdaran
- Men's Health and Reproductive Health Research CenterShahid Beheshti University of Medical SciencesTehranIran
| | - Hamid Abdollahi
- Department of Radiologic Technology, Faculty of Allied MedicineKerman University of Medical SciencesKermanIran
| | - Amir Reza Radmard
- Department of RadiologyShariati Hospital, Tehran University of Medical SciencesTehranIran
| | - Kiara Rezaei‐Kalantari
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Mostafa Ghelich Oghli
- Research and Development DepartmentMed Fanavaran Plus Co.KarajIran
- Department of Cardiovascular SciencesKU LeuvenLeuvenBelgium
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular ImagingGeneva University HospitalGenevaSwitzerland
- Geneva University NeurocenterGeneva UniversityGenevaSwitzerland
- Department of Nuclear Medicine and Molecular ImagingUniversity of Groningen, University Medical Center GroningenGroningenNetherlands
- Department of Nuclear MedicineUniversity of Southern DenmarkOdenseDenmark
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Salimi Y, Shiri I, Akhavanallaf A, Mansouri Z, Saberi Manesh A, Sanaat A, Pakbin M, Askari D, Sandoughdaran S, Sharifipour E, Arabi H, Zaidi H. Deep learning-based fully automated Z-axis coverage range definition from scout scans to eliminate overscanning in chest CT imaging. Insights Imaging 2021; 12:162. [PMID: 34743251 PMCID: PMC8572075 DOI: 10.1186/s13244-021-01105-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/09/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Despite the prevalence of chest CT in the clinic, concerns about unoptimized protocols delivering high radiation doses to patients still remain. This study aimed to assess the additional radiation dose associated with overscanning in chest CT and to develop an automated deep learning-assisted scan range selection technique to reduce radiation dose to patients. RESULTS A significant overscanning range (31 ± 24) mm was observed in clinical setting for over 95% of the cases. The average Dice coefficient for lung segmentation was 0.96 and 0.97 for anterior-posterior (AP) and lateral projections, respectively. By considering the exact lung coverage as the ground truth, and AP and lateral projections as input, The DL-based approach resulted in errors of 0.08 ± 1.46 and - 1.5 ± 4.1 mm in superior and inferior directions, respectively. In contrast, the error on external scout views was - 0.7 ± 4.08 and 0.01 ± 14.97 mm for superior and inferior directions, respectively.The ED reduction achieved by automated scan range selection was 21% in the test group. The evaluation of a large multi-centric chest CT dataset revealed unnecessary ED of more than 2 mSv per scan and 67% increase in the thyroid absorbed dose. CONCLUSION The proposed DL-based solution outperformed previous automatic methods with acceptable accuracy, even in complicated and challenging cases. The generizability of the model was demonstrated by fine-tuning the model on AP scout views and achieving acceptable results. The method can reduce the unoptimized dose to patients by exclunding unnecessary organs from field of view.
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Affiliation(s)
- Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Zahra Mansouri
- Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abdollah Saberi Manesh
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Amirhossein Sanaat
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Masoumeh Pakbin
- Imaging Department, Qom University of Medical Sciences, Qom, Iran
| | - Dariush Askari
- Department of Radiology Technology, Shahid Beheshti University of Medical, Tehran, Iran
| | - Saleh Sandoughdaran
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Sharifipour
- Neuroscience Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, 1211, Geneva, Switzerland.
- Geneva University Neurocenter, Geneva University, Geneva, Switzerland.
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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Akhavanallaf A, Mohammadi R, Shiri I, Salimi Y, Arabi H, Zaidi H. Personalized brachytherapy dose reconstruction using deep learning. Comput Biol Med 2021; 136:104755. [PMID: 34388458 DOI: 10.1016/j.compbiomed.2021.104755] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND PURPOSE Accurate calculation of the absorbed dose delivered to the tumor and normal tissues improves treatment gain factor, which is the major advantage of brachytherapy over external radiation therapy. To address the simplifications of TG-43 assumptions that ignore the dosimetric impact of medium heterogeneities, we proposed a deep learning (DL)-based approach, which improves the accuracy while requiring a reasonable computation time. MATERIALS AND METHODS We developed a Monte Carlo (MC)-based personalized brachytherapy dosimetry simulator (PBrDoseSim), deployed to generate patient-specific dose distributions. A deep neural network (DNN) was trained to predict personalized dose distributions derived from MC simulations, serving as ground truth. The paired channel input used for the training is composed of dose distribution kernel in water medium along with the full-volumetric density maps obtained from CT images reflecting medium heterogeneity. RESULTS The predicted single-dwell dose kernels were in good agreement with MC-based kernels serving as reference, achieving a mean relative absolute error (MRAE) and mean absolute error (MAE) of 1.16 ± 0.42% and 4.2 ± 2.7 × 10-4 (Gy.sec-1/voxel), respectively. The MRAE of the dose volume histograms (DVHs) between the DNN and MC calculations in the clinical target volume were 1.8 ± 0.86%, 0.56 ± 0.56%, and 1.48 ± 0.72% for D90, V150, and V100, respectively. For bladder, sigmoid, and rectum, the MRAE of D5cc between the DNN and MC calculations were 2.7 ± 1.7%, 1.9 ± 1.3%, and 2.1 ± 1.7%, respectively. CONCLUSION The proposed DNN-based personalized brachytherapy dosimetry approach exhibited comparable performance to the MC method while overcoming the computational burden of MC calculations and oversimplifications of TG-43.
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Affiliation(s)
- Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Reza Mohammadi
- Department of Medical Physics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva 4, Switzerland; Geneva University Neurocenter, Geneva University, CH-1205, Geneva, Switzerland; Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, Netherlands; Department of Nuclear Medicine, University of Southern Denmark, DK-500, Odense, Denmark.
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Shiri I, Sorouri M, Geramifar P, Nazari M, Abdollahi M, Salimi Y, Khosravi B, Askari D, Aghaghazvini L, Hajianfar G, Kasaeian A, Abdollahi H, Arabi H, Rahmim A, Radmard AR, Zaidi H. Machine learning-based prognostic modeling using clinical data and quantitative radiomic features from chest CT images in COVID-19 patients. Comput Biol Med 2021; 132:104304. [PMID: 33691201 PMCID: PMC7925235 DOI: 10.1016/j.compbiomed.2021.104304] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To develop prognostic models for survival (alive or deceased status) prediction of COVID-19 patients using clinical data (demographics and history, laboratory tests, visual scoring by radiologists) and lung/lesion radiomic features extracted from chest CT images. METHODS Overall, 152 patients were enrolled in this study protocol. These were divided into 106 training/validation and 46 test datasets (untouched during training), respectively. Radiomic features were extracted from the segmented lungs and infectious lesions separately from chest CT images. Clinical data, including patients' history and demographics, laboratory tests and radiological scores were also collected. Univariate analysis was first performed (q-value reported after false discovery rate (FDR) correction) to determine the most predictive features among all imaging and clinical data. Prognostic modeling of survival was performed using radiomic features and clinical data, separately or in combination. Maximum relevance minimum redundancy (MRMR) and XGBoost were used for feature selection and classification. The receiver operating characteristic (ROC) curve and the area under the ROC curve (AUC), sensitivity, specificity, and accuracy were used to assess the prognostic performance of the models on the test datasets. RESULTS For clinical data, cancer comorbidity (q-value < 0.01), consciousness level (q-value < 0.05) and radiological score involved zone (q-value < 0.02) were found to have high correlated features with outcome. Oxygen saturation (AUC = 0.73, q-value < 0.01) and Blood Urea Nitrogen (AUC = 0.72, q-value = 0.72) were identified as high clinical features. For lung radiomic features, SAHGLE (AUC = 0.70) and HGLZE (AUC = 0.67) from GLSZM were identified as most prognostic features. Amongst lesion radiomic features, RLNU from GLRLM (AUC = 0.73), HGLZE from GLSZM (AUC = 0.73) had the highest performance. In multivariate analysis, combining lung, lesion and clinical features was determined to provide the most accurate prognostic model (AUC = 0.95 ± 0.029 (95%CI: 0.95-0.96), accuracy = 0.88 ± 0.046 (95% CI: 0.88-0.89), sensitivity = 0.88 ± 0.066 (95% CI = 0.87-0.9) and specificity = 0.89 ± 0.07 (95% CI = 0.87-0.9)). CONCLUSION Combination of radiomic features and clinical data can effectively predict outcome in COVID-19 patients. The developed model has significant potential for improved management of COVID-19 patients.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Majid Sorouri
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parham Geramifar
- Research Center for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Nazari
- Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Abdollahi
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Bardia Khosravi
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Dariush Askari
- Department of Radiology Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Aghaghazvini
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghasem Hajianfar
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Kasaeian
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran,Hematology, Oncology and Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Abdollahi
- Department of Radiologic Sciences and Medical Physics, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Arman Rahmim
- Departments of Radiology and Physics, University of British Columbia, Vancouver, BC, Canada,Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Amir Reza Radmard
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran,Corresponding author. Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland,Geneva University Neurocenter, Geneva University, Geneva, Switzerland,Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands,Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark,Corresponding author. Geneva University Hospital, Division of Nuclear Medicine and Molecular Imaging, CH-1211, Geneva, Switzerland
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Shiri I, Akhavanallaf A, Sanaat A, Salimi Y, Askari D, Mansouri Z, Shayesteh SP, Hasanian M, Rezaei-Kalantari K, Salahshour A, Sandoughdaran S, Abdollahi H, Arabi H, Zaidi H. Ultra-low-dose chest CT imaging of COVID-19 patients using a deep residual neural network. Eur Radiol 2021; 31:1420-1431. [PMID: 32879987 PMCID: PMC7467843 DOI: 10.1007/s00330-020-07225-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/13/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVES The current study aimed to design an ultra-low-dose CT examination protocol using a deep learning approach suitable for clinical diagnosis of COVID-19 patients. METHODS In this study, 800, 170, and 171 pairs of ultra-low-dose and full-dose CT images were used as input/output as training, test, and external validation set, respectively, to implement the full-dose prediction technique. A residual convolutional neural network was applied to generate full-dose from ultra-low-dose CT images. The quality of predicted CT images was assessed using root mean square error (RMSE), structural similarity index (SSIM), and peak signal-to-noise ratio (PSNR). Scores ranging from 1 to 5 were assigned reflecting subjective assessment of image quality and related COVID-19 features, including ground glass opacities (GGO), crazy paving (CP), consolidation (CS), nodular infiltrates (NI), bronchovascular thickening (BVT), and pleural effusion (PE). RESULTS The radiation dose in terms of CT dose index (CTDIvol) was reduced by up to 89%. The RMSE decreased from 0.16 ± 0.05 to 0.09 ± 0.02 and from 0.16 ± 0.06 to 0.08 ± 0.02 for the predicted compared with ultra-low-dose CT images in the test and external validation set, respectively. The overall scoring assigned by radiologists showed an acceptance rate of 4.72 ± 0.57 out of 5 for reference full-dose CT images, while ultra-low-dose CT images rated 2.78 ± 0.9. The predicted CT images using the deep learning algorithm achieved a score of 4.42 ± 0.8. CONCLUSIONS The results demonstrated that the deep learning algorithm is capable of predicting standard full-dose CT images with acceptable quality for the clinical diagnosis of COVID-19 positive patients with substantial radiation dose reduction. KEY POINTS • Ultra-low-dose CT imaging of COVID-19 patients would result in the loss of critical information about lesion types, which could potentially affect clinical diagnosis. • Deep learning-based prediction of full-dose from ultra-low-dose CT images for the diagnosis of COVID-19 could reduce the radiation dose by up to 89%. • Deep learning algorithms failed to recover the correct lesion structure/density for a number of patients considered outliers, and as such, further research and development is warranted to address these limitations.
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Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Azadeh Akhavanallaf
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Amirhossein Sanaat
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Yazdan Salimi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Dariush Askari
- Department of Radiology Technology, Shahid Beheshti University of Medical, Tehran, Iran
| | - Zahra Mansouri
- Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sajad P Shayesteh
- Department of Physiology, Pharmacology and Medical Physics, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Hasanian
- Department of Radiology, Arak University of Medical Sciences, Arak, Iran
| | - Kiara Rezaei-Kalantari
- Rajaie Cardiovascular, Medical & Research Center, Iran University of Medical Science, Tehran, Iran
| | - Ali Salahshour
- Department of Radiology, Alborz University of Medical Sciences, Karaj, Iran
| | - Saleh Sandoughdaran
- Department of Radiation Oncology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Abdollahi
- Department of Radiologic Sciences and Medical Physics, Faculty of Allied Medicine, Kerman University of Medical sciences, Kerman, Iran
| | - Hossein Arabi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland.
- Geneva University Neurocenter, Geneva University, CH-1205, Geneva, Switzerland.
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark.
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Deevband M, Ghorbani M, Eshraghi A, Salimi Y, Saeedzadeh E, Kardan M, Sadeghi S, Divband D, Ahmadi M. Patient effective dose estimation for routine computed tomography examinations in Iran. INT J RADIAT RES 2021. [DOI: 10.29252/ijrr.19.1.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Asadi-Lari M, Salimi Y, Vaez-Mahdavi MR, Faghihzadeh S, Haeri Mehrizi AA, Jorjoran Shushtari Z, Cheraghian B. Socio-Economic Status and Prevalence of Self-Reported Osteoporosis in Tehran: Results from a Large Population-Based Cross-Sectional Study (Urban HEART-2). J Urban Health 2018; 95:682-690. [PMID: 29637433 PMCID: PMC6181817 DOI: 10.1007/s11524-018-0246-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Osteoporosis is a widespread disease among older peoples. The aim of this study is to estimate the prevalence of self-reported osteoporosis and assessing its association with socio-economic status. A population-based cross-sectional study was conducted in Tehran, Iran in 2011. Participants were 45,990 individuals aged above 20 years from 22 urban districts. Osteoporosis was measured by self-administrative questionnaire. Wealth index was constructed using principal component analysis based on household assets. Chi-square test, chi square test for trend, and crude odds ratio were used to assess associations in univariate analysis. Multiple logistic regression utilized to estimate adjusted associations between self-reported osteoporosis and socio-economic status.The overall estimated prevalence of self-reported osteoporosis was 4% (95% CI 3.88-4.13), 1.19% in men, and 6.84% in women (P < 0.001). The prevalence increased considerably as age increased (P for trend < 0.001). In multivariable analysis, education and wealth status were negative, and smoking was positively associated with the prevalence of self-reported osteoporosis. No association was found between participants' skill levels and Townsend deprivation index with the prevalence of self-reported osteoporosis.The findings of the present study have improved understanding of the association between socioeconomic status and osteoporosis in the Iranian population. It is important to consider socioeconomic status in screening and prevention programs.
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Affiliation(s)
- M Asadi-Lari
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
- Oncopathology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Y Salimi
- Department of Epidemiology and Biostatistics, School of Public Health, Kermanshah University of Medical Science, Kermanshah, Iran
| | | | - S Faghihzadeh
- Department of Social Medicine, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - A A Haeri Mehrizi
- Health Education and Promotion Research Group, Health Metrics Research Center, Iranian Institute for Health Sciences Research, ACECR, Tehran, Iran
| | - Z Jorjoran Shushtari
- Determinants of Health, Social Determinants of Health Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Bahman Cheraghian
- Department of Epidemiology and Biostatistics, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Abdollahpour I, Salimi Y. Dietary patterns and the risk of coronary heart disease among Jordanians: A case-control study. Statistical and methodological issue. Nutr Metab Cardiovasc Dis 2018; 28:531-532. [PMID: 29665994 DOI: 10.1016/j.numecd.2018.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 01/15/2018] [Accepted: 02/05/2018] [Indexed: 11/24/2022]
Affiliation(s)
- I Abdollahpour
- Department of Epidemiology, School of Public Health, Arak University of Medical Sciences, Arak, Iran.
| | - Y Salimi
- Social Development & Health Promotion Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Sajjadi H, Jorjoran Shushtari Z, Mahboubi S, Rafiey H, Salimi Y. Effect of socio-economic status, family smoking and mental health through social network on the substance use potential in adolescents: a mediation analysis. Public Health 2018; 157:14-19. [PMID: 29475107 DOI: 10.1016/j.puhe.2018.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 10/18/2022]
Abstract
OBJECTIVES Understanding pathways that influence substance use potential (SUP) can help with effective substance use prevention interventions among adolescents. The aim of the present study is to contribute to a better understanding of the SUP of adolescents by examining the mediating role of social network quality in the SUP of Iranian adolescents. STUDY DESIGN A cross-sectional study. METHODS Structural equation modeling was conducted to assess the hypothesized model that social network quality would mediate the association of family socio-economic status, a mental health disorder, and family smoking with addiction potential. RESULTS The model shows a good fit to the data. Social network quality mediated the effect of family smoking on the SUP for boys. A mental health disorder had a positive significant direct effect on addiction potential for both girls and boys. CONCLUSIONS Social network quality mediates the effect of family smoking on boys' addiction potential in the context of Iran. Educational programs based on local societal ways and cultural norms are recommended to change tobacco smoking behavior among family members. In addition, to prevent subsequent substance use among adolescents, more effort is needed to improve their mental health.
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Affiliation(s)
- H Sajjadi
- Social Welfare Management Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Z Jorjoran Shushtari
- Student research committee, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - S Mahboubi
- Department of Social Welfare Management, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H Rafiey
- Social Welfare Management Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Y Salimi
- Department of Epidemiology, School of Public Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Abdollahi H, Shiri I, Salimi Y, Sarebani M, Mehdinia R, Deevband MR, Mahdavi SR, Sohrabi A, Bitarafan-Rajabi A. Radiation dose in cardiac SPECT/CT: An estimation of SSDE and effective dose. Eur J Radiol 2016; 85:2257-2261. [PMID: 27842674 DOI: 10.1016/j.ejrad.2016.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/11/2016] [Accepted: 10/19/2016] [Indexed: 12/21/2022]
Abstract
AIMS The dose levels for Computed Tomography (CT) localization and attenuation correction of Single Photon Emission Computed Tomography (SPECT) are limited and reported as Volume Computed Tomography Dose Index (CTDIvol) and Dose-Length Product (DLP). This work presents CT dose estimation from Cardiac SPECT/CT based on new American Association of Physicists in Medicine (AAPM) Size Specific Dose Estimation (SSDE) parameter, effective dose, organ doses and also emission dose from nuclear issue. MATERIAL AND METHODS Myocardial perfusion SPECT/CT for 509 patients was included in the study. SSDE, effective dose and organ dose were calculated using AAPM guideline and Impact-Dose software. Data were analyzed using R and SPSS statistical software. Spearman-Pearson correlation test and linear regression models were used for finding correlations and relationships among parameters. RESULTS The mean CTDIvol was 1.34 mGy±0.19 and the mean SSDE was 1.7 mGy±0.16. The mean±SD of effective dose from emission, CT and total dose were 11.5±1.4, 0.49±0.11 and 12.67±1.73 (mSv) respectively. The mean±SD of effective dose from emission, CT and total dose were 11.5±1.4, 0.49±0.11 and 12.67±1.73 (mSv) respectively. The spearman test showed that correlation between body size and organ doses is significant except thyroid and red bone marrow. CTDIvol was strongly dependent on patient size, but SSDE was not. Emission dose was strongly dependent on patient weight, but its dependency was lower to effective diameter. CONCLUSION The dose parameters including CTDIvol, DLP, SSDE, effective dose values reported here are very low and below the reference level. This data suggest that appropriate CT acquisition parameters in SPECT/CT localization and attenuation correction are very beneficial for patients and lowering cancer risks.
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Affiliation(s)
- Hamid Abdollahi
- Department of Medical Physics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Isaac Shiri
- Department of Medical Physics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Yazdan Salimi
- Biomedical Engineering and Medical Physics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maghsoud Sarebani
- Department of Medical Physics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Mehdinia
- Department of Medical Physics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Deevband
- Biomedical Engineering and Medical Physics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seied Rabi Mahdavi
- Department of Medical Physics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Radiation Biology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Sohrabi
- Department of Biostatistics, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Bitarafan-Rajabi
- Department of Medical Physics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Nuclear Medicine, Rajaei Cardiovascular, Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
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