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Barufaldi B, Gomes JV, Filho TS, do Rêgo TG, Malheiros Y, Vent TL, Gastounioti A, Maidment A. Assessment of Volumetric Dense Tissue Segmentation in Tomosynthesis Using Deep Virtual Clinical Trials. Pattern Recognit 2024; 153:110494. [PMID: 38706638 PMCID: PMC11065113 DOI: 10.1016/j.patcog.2024.110494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
The adoption of artificial intelligence (AI) in medical imaging requires careful evaluation of machine-learning algorithms. We propose the use of a "deep virtual clinical trial" (DeepVCT) method to effectively evaluate the performance of AI algorithms. In this paper, DeepVCTs have been proposed to elucidate limitations of AI applications and predictions of clinical outcomes, avoiding biases in study designs. The DeepVCT method was used to evaluate the performance of nnU-Net models in assessing volumetric breast density (VBD) from digital breast tomosynthesis (DBT) images. In total, 2,010 anatomical breast models were simulated. Projections were simulated using the acquisition geometry of a clinical DBT system. The projections were reconstructed using 0.1, 0.2, and 0.5 mm plane spacing. nnU-Net models were developed using the center-most planes of the reconstructions with the respective ground-truth. The results show that the accuracy of the nnU-Net improves significantly with DBT images reconstructed with 0.1 mm plane spacing (78.4×205.3×40.1 mm3). The segmentations resulted in Dice values up to 0.84 with area under the receiver operating characteristic curve of 0.92. The optimization of plane spacing for VBD assessment was used as an exemplar of a DeepVCT application, allowing us to interpret better the input parameters and outcomes of the nnU-Net. Thus, DeepVCTs can provide a plethora of evidence to predict the efficacy of these algorithms using large-scale simulation-based data.
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Affiliation(s)
- B Barufaldi
- Department of Radiology, University of Pennsylvania, 3640 Hamilton Walk, PA 19104, United States
| | - J V Gomes
- Center of Informatics, Federal University of Paraíba, Rua dos Escoteiros s/n, João Pessoa, PB 58058-600, Brazil
| | - Tm Silva Filho
- Department of Statistics, Federal University of Paraíba, Campus I - Jardim Cidade Universitária, João Pessoa - PB, 58051-090, Brazil
| | - T G do Rêgo
- Center of Informatics, Federal University of Paraíba, Rua dos Escoteiros s/n, João Pessoa, PB 58058-600, Brazil
| | - Y Malheiros
- Center of Informatics, Federal University of Paraíba, Rua dos Escoteiros s/n, João Pessoa, PB 58058-600, Brazil
| | - T L Vent
- Department of Radiology, University of Pennsylvania, 3640 Hamilton Walk, PA 19104, United States
| | - A Gastounioti
- Department of Radiology, University of Pennsylvania, 3640 Hamilton Walk, PA 19104, United States
| | - Ada Maidment
- Department of Radiology, University of Pennsylvania, 3640 Hamilton Walk, PA 19104, United States
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McNitt-Gray M, Napel S, Jaggi A, Mattonen SA, Hadjiiski L, Muzi M, Goldgof D, Balagurunathan Y, Pierce LA, Kinahan PE, Jones EF, Nguyen A, Virkud A, Chan HP, Emaminejad N, Wahi-Anwar M, Daly M, Abdalah M, Yang H, Lu L, Lv W, Rahmim A, Gastounioti A, Pati S, Bakas S, Kontos D, Zhao B, Kalpathy-Cramer J, Farahani K. Standardization in Quantitative Imaging: A Multicenter Comparison of Radiomic Features from Different Software Packages on Digital Reference Objects and Patient Data Sets. ACTA ACUST UNITED AC 2021; 6:118-128. [PMID: 32548288 PMCID: PMC7289262 DOI: 10.18383/j.tom.2019.00031] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [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] [Indexed: 11/24/2022]
Abstract
Radiomic features are being increasingly studied for clinical applications. We aimed to assess the agreement among radiomic features when computed by several groups by using different software packages under very tightly controlled conditions, which included standardized feature definitions and common image data sets. Ten sites (9 from the NCI's Quantitative Imaging Network] positron emission tomography–computed tomography working group plus one site from outside that group) participated in this project. Nine common quantitative imaging features were selected for comparison including features that describe morphology, intensity, shape, and texture. The common image data sets were: three 3D digital reference objects (DROs) and 10 patient image scans from the Lung Image Database Consortium data set using a specific lesion in each scan. Each object (DRO or lesion) was accompanied by an already-defined volume of interest, from which the features were calculated. Feature values for each object (DRO or lesion) were reported. The coefficient of variation (CV), expressed as a percentage, was calculated across software packages for each feature on each object. Thirteen sets of results were obtained for the DROs and patient data sets. Five of the 9 features showed excellent agreement with CV < 1%; 1 feature had moderate agreement (CV < 10%), and 3 features had larger variations (CV ≥ 10%) even after attempts at harmonization of feature calculations. This work highlights the value of feature definition standardization as well as the need to further clarify definitions for some features.
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Affiliation(s)
- M McNitt-Gray
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - S Napel
- Stanford University School of Medicine, Stanford, CA
| | - A Jaggi
- Stanford University School of Medicine, Stanford, CA
| | - S A Mattonen
- Stanford University School of Medicine, Stanford, CA.,The University of Western Ontario, Canada
| | | | - M Muzi
- University of Washington, Seattle, WA
| | - D Goldgof
- University of South Florida, Tampa, FL
| | | | | | | | - E F Jones
- UC San Francisco, School of Medicine, San Francisco, CA
| | - A Nguyen
- UC San Francisco, School of Medicine, San Francisco, CA
| | - A Virkud
- University of Michigan, Ann Arbor, MI
| | - H P Chan
- University of Michigan, Ann Arbor, MI
| | - N Emaminejad
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - M Wahi-Anwar
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - M Daly
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - M Abdalah
- H. Lee Moffitt Cancer Center, Tampa, FL
| | - H Yang
- Columbia University Medical Center, New York, NY
| | - L Lu
- Columbia University Medical Center, New York, NY
| | - W Lv
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - A Rahmim
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - A Gastounioti
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA
| | - S Pati
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA
| | - S Bakas
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA
| | - D Kontos
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA
| | - B Zhao
- Columbia University Medical Center, New York, NY
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Kadoglou NP, Sfyroeras GS, Spathis A, Gkekas C, Gastounioti A, Mantas G, Nikita KS, Karakitsos P, Liapis CD. Re: 'response to letter to the editor on "Galectin-3, carotid plaque vulnerability, and potential effects of statin therapy"'. Eur J Vasc Endovasc Surg 2015; 49:613-4. [PMID: 25784505 DOI: 10.1016/j.ejvs.2015.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 10/23/2022]
Affiliation(s)
- N P Kadoglou
- Department of Vascular Surgery, Medical School, University of Athens, Athens, Greece.
| | - G S Sfyroeras
- Department of Vascular Surgery, Medical School, University of Athens, Athens, Greece
| | - A Spathis
- Department of Cytopathology, "Attikon" University Hospital, Athens, Greece
| | - C Gkekas
- Department of Vascular Surgery, Medical School, University of Athens, Athens, Greece
| | - A Gastounioti
- School of Electrical and Computer Engineering, National Technical University of Athens, Athens, Greece
| | - G Mantas
- Department of Vascular Surgery, Medical School, University of Athens, Athens, Greece
| | - K S Nikita
- School of Electrical and Computer Engineering, National Technical University of Athens, Athens, Greece
| | - P Karakitsos
- Department of Cytopathology, "Attikon" University Hospital, Athens, Greece
| | - C D Liapis
- Department of Vascular Surgery, Medical School, University of Athens, Athens, Greece
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Kadoglou N, Sfyroeras G, Spathis A, Gkekas C, Gastounioti A, Mantas G, Nikita K, Karakitsos P, Liapis C. Galectin-3, Carotid Plaque Vulnerability, and Potential Effects of Statin Therapy. Eur J Vasc Endovasc Surg 2015; 49:4-9. [DOI: 10.1016/j.ejvs.2014.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/13/2014] [Indexed: 11/30/2022]
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Gastounioti A, Golemati S, Stoitsis JS, Nikita KS. Carotid artery wall motion analysis from B-mode ultrasound using adaptive block matching: in silico evaluation and in vivo application. Phys Med Biol 2013; 58:8647-61. [PMID: 24256708 DOI: 10.1088/0031-9155/58/24/8647] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Valid risk stratification for carotid atherosclerotic plaques represents a crucial public health issue toward preventing fatal cerebrovascular events. Although motion analysis (MA) provides useful information about arterial wall dynamics, the identification of motion-based risk markers remains a significant challenge. Considering that the ability of a motion estimator (ME) to handle changes in the appearance of motion targets has a major effect on accuracy in MA, we investigated the potential of adaptive block matching (ABM) MEs, which consider changes in image intensities over time. To assure the validity in MA, we optimized and evaluated the ABM MEs in the context of a specially designed in silico framework. ABM(FIRF2), which takes advantage of the periodicity characterizing the arterial wall motion, was the most effective ABM algorithm, yielding a 47% accuracy increase with respect to the conventional block matching. The in vivo application of ABM(FIRF2) revealed five potential risk markers: low movement amplitude of the normal part of the wall adjacent to the plaques in the radial (RMA(PWL)) and longitudinal (LMA(PWL)) directions, high radial motion amplitude of the plaque top surface (RMA(PTS)), and high relative movement, expressed in terms of radial strain (RSI(PL)) and longitudinal shear strain (LSSI(PL)), between plaque top and bottom surfaces. The in vivo results were reproduced by OF(LK(WLS)) and ABM(KF-K2), MEs previously proposed by the authors and with remarkable in silico performances, thereby reinforcing the clinical values of the markers and the potential of those MEs. Future in vivo studies will elucidate with confidence the full potential of the markers.
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Affiliation(s)
- A Gastounioti
- Biomedical Simulations and Imaging Laboratory, National Technical University of Athens, Greece
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