Deep convolutional neural networks with multiplane consensus labeling for lung function quantification using UTE proton MRI

Background Ultrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development of rapid biomarker extraction and regional quantification has lagged behind due to labor‐intensive lung segmentation. Purpose To evaluate a...

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Published in:Journal of magnetic resonance imaging Vol. 50; no. 4; pp. 1169 - 1181
Main Authors: Zha, Wei, Fain, Sean B., Schiebler, Mark L., Evans, Michael D., Nagle, Scott K., Liu, Fang
Format: Journal Article
Language:English
Published: Hoboken, USA John Wiley & Sons, Inc 01.10.2019
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ISSN:1053-1807, 1522-2586, 1522-2586
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Abstract Background Ultrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development of rapid biomarker extraction and regional quantification has lagged behind due to labor‐intensive lung segmentation. Purpose To evaluate a deep learning (DL) approach for automated lung segmentation to extract image‐based biomarkers from functional lung imaging using 3D radial UTE oxygen‐enhanced (OE) MRI. Study Type Retrospective study aimed to evaluate a technical development. Population Forty‐five human subjects, including 16 healthy volunteers, 5 asthma, and 24 patients with cystic fibrosis. Field Strength/Sequence 1.5T MRI, 3D radial UTE (TE = 0.08 msec) sequence. Assessment Two 3D radial UTE volumes were acquired sequentially under normoxic (21% O2) and hyperoxic (100% O2) conditions. Automated segmentation of the lungs using 2D convolutional encoder‐decoder based DL method, and the subsequent functional quantification via adaptive K‐means were compared with the results obtained from the reference method, supervised region growing. Statistical Tests Relative to the reference method, the performance of DL on volumetric quantification was assessed using Dice coefficient with 95% confidence interval (CI) for accuracy, two‐sided Wilcoxon signed‐rank test for computation time, and Bland–Altman analysis on the functional measure derived from the OE images. Results The DL method produced strong agreement with supervised region growing for the right (Dice: 0.97; 95% CI = [0.96, 0.97]; P < 0.001) and left lungs (Dice: 0.96; 95% CI = [0.96, 0.97]; P < 0.001). The DL method averaged 46 seconds to generate the automatic segmentations in contrast to 1.93 hours using the reference method (P < 0.001). Bland–Altman analysis showed nonsignificant intermethod differences of volumetric (P ≥ 0.12) and functional measurements (P ≥ 0.34) in the left and right lungs. Data Conclusion DL provides rapid, automated, and robust lung segmentation for quantification of regional lung function using UTE proton MRI. Level of Evidence: 2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;50:1169–1181.
AbstractList BackgroundUltrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development of rapid biomarker extraction and regional quantification has lagged behind due to labor‐intensive lung segmentation.PurposeTo evaluate a deep learning (DL) approach for automated lung segmentation to extract image‐based biomarkers from functional lung imaging using 3D radial UTE oxygen‐enhanced (OE) MRI.Study TypeRetrospective study aimed to evaluate a technical development.PopulationForty‐five human subjects, including 16 healthy volunteers, 5 asthma, and 24 patients with cystic fibrosis.Field Strength/Sequence1.5T MRI, 3D radial UTE (TE = 0.08 msec) sequence.AssessmentTwo 3D radial UTE volumes were acquired sequentially under normoxic (21% O2) and hyperoxic (100% O2) conditions. Automated segmentation of the lungs using 2D convolutional encoder‐decoder based DL method, and the subsequent functional quantification via adaptive K‐means were compared with the results obtained from the reference method, supervised region growing.Statistical TestsRelative to the reference method, the performance of DL on volumetric quantification was assessed using Dice coefficient with 95% confidence interval (CI) for accuracy, two‐sided Wilcoxon signed‐rank test for computation time, and Bland–Altman analysis on the functional measure derived from the OE images.ResultsThe DL method produced strong agreement with supervised region growing for the right (Dice: 0.97; 95% CI = [0.96, 0.97]; P < 0.001) and left lungs (Dice: 0.96; 95% CI = [0.96, 0.97]; P < 0.001). The DL method averaged 46 seconds to generate the automatic segmentations in contrast to 1.93 hours using the reference method (P < 0.001). Bland–Altman analysis showed nonsignificant intermethod differences of volumetric (P ≥ 0.12) and functional measurements (P ≥ 0.34) in the left and right lungs.Data ConclusionDL provides rapid, automated, and robust lung segmentation for quantification of regional lung function using UTE proton MRI.Level of Evidence: 2Technical Efficacy: Stage 1J. Magn. Reson. Imaging 2019;50:1169–1181.
Background Ultrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development of rapid biomarker extraction and regional quantification has lagged behind due to labor‐intensive lung segmentation. Purpose To evaluate a deep learning (DL) approach for automated lung segmentation to extract image‐based biomarkers from functional lung imaging using 3D radial UTE oxygen‐enhanced (OE) MRI. Study Type Retrospective study aimed to evaluate a technical development. Population Forty‐five human subjects, including 16 healthy volunteers, 5 asthma, and 24 patients with cystic fibrosis. Field Strength/Sequence 1.5T MRI, 3D radial UTE (TE = 0.08 msec) sequence. Assessment Two 3D radial UTE volumes were acquired sequentially under normoxic (21% O2) and hyperoxic (100% O2) conditions. Automated segmentation of the lungs using 2D convolutional encoder‐decoder based DL method, and the subsequent functional quantification via adaptive K‐means were compared with the results obtained from the reference method, supervised region growing. Statistical Tests Relative to the reference method, the performance of DL on volumetric quantification was assessed using Dice coefficient with 95% confidence interval (CI) for accuracy, two‐sided Wilcoxon signed‐rank test for computation time, and Bland–Altman analysis on the functional measure derived from the OE images. Results The DL method produced strong agreement with supervised region growing for the right (Dice: 0.97; 95% CI = [0.96, 0.97]; P < 0.001) and left lungs (Dice: 0.96; 95% CI = [0.96, 0.97]; P < 0.001). The DL method averaged 46 seconds to generate the automatic segmentations in contrast to 1.93 hours using the reference method (P < 0.001). Bland–Altman analysis showed nonsignificant intermethod differences of volumetric (P ≥ 0.12) and functional measurements (P ≥ 0.34) in the left and right lungs. Data Conclusion DL provides rapid, automated, and robust lung segmentation for quantification of regional lung function using UTE proton MRI. Level of Evidence: 2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;50:1169–1181.
Ultrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development of rapid biomarker extraction and regional quantification has lagged behind due to labor-intensive lung segmentation. To evaluate a deep learning (DL) approach for automated lung segmentation to extract image-based biomarkers from functional lung imaging using 3D radial UTE oxygen-enhanced (OE) MRI. Retrospective study aimed to evaluate a technical development. Forty-five human subjects, including 16 healthy volunteers, 5 asthma, and 24 patients with cystic fibrosis. 1.5T MRI, 3D radial UTE (TE = 0.08 msec) sequence. Two 3D radial UTE volumes were acquired sequentially under normoxic (21% O ) and hyperoxic (100% O ) conditions. Automated segmentation of the lungs using 2D convolutional encoder-decoder based DL method, and the subsequent functional quantification via adaptive K-means were compared with the results obtained from the reference method, supervised region growing. Relative to the reference method, the performance of DL on volumetric quantification was assessed using Dice coefficient with 95% confidence interval (CI) for accuracy, two-sided Wilcoxon signed-rank test for computation time, and Bland-Altman analysis on the functional measure derived from the OE images. The DL method produced strong agreement with supervised region growing for the right (Dice: 0.97; 95% CI = [0.96, 0.97]; P < 0.001) and left lungs (Dice: 0.96; 95% CI = [0.96, 0.97]; P < 0.001). The DL method averaged 46 seconds to generate the automatic segmentations in contrast to 1.93 hours using the reference method (P < 0.001). Bland-Altman analysis showed nonsignificant intermethod differences of volumetric (P ≥ 0.12) and functional measurements (P ≥ 0.34) in the left and right lungs. DL provides rapid, automated, and robust lung segmentation for quantification of regional lung function using UTE proton MRI. 2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;50:1169-1181.
Ultrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development of rapid biomarker extraction and regional quantification has lagged behind due to labor-intensive lung segmentation.BACKGROUNDUltrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development of rapid biomarker extraction and regional quantification has lagged behind due to labor-intensive lung segmentation.To evaluate a deep learning (DL) approach for automated lung segmentation to extract image-based biomarkers from functional lung imaging using 3D radial UTE oxygen-enhanced (OE) MRI.PURPOSETo evaluate a deep learning (DL) approach for automated lung segmentation to extract image-based biomarkers from functional lung imaging using 3D radial UTE oxygen-enhanced (OE) MRI.Retrospective study aimed to evaluate a technical development.STUDY TYPERetrospective study aimed to evaluate a technical development.Forty-five human subjects, including 16 healthy volunteers, 5 asthma, and 24 patients with cystic fibrosis.POPULATIONForty-five human subjects, including 16 healthy volunteers, 5 asthma, and 24 patients with cystic fibrosis.1.5T MRI, 3D radial UTE (TE = 0.08 msec) sequence.FIELD STRENGTH/SEQUENCE1.5T MRI, 3D radial UTE (TE = 0.08 msec) sequence.Two 3D radial UTE volumes were acquired sequentially under normoxic (21% O2 ) and hyperoxic (100% O2 ) conditions. Automated segmentation of the lungs using 2D convolutional encoder-decoder based DL method, and the subsequent functional quantification via adaptive K-means were compared with the results obtained from the reference method, supervised region growing.ASSESSMENTTwo 3D radial UTE volumes were acquired sequentially under normoxic (21% O2 ) and hyperoxic (100% O2 ) conditions. Automated segmentation of the lungs using 2D convolutional encoder-decoder based DL method, and the subsequent functional quantification via adaptive K-means were compared with the results obtained from the reference method, supervised region growing.Relative to the reference method, the performance of DL on volumetric quantification was assessed using Dice coefficient with 95% confidence interval (CI) for accuracy, two-sided Wilcoxon signed-rank test for computation time, and Bland-Altman analysis on the functional measure derived from the OE images.STATISTICAL TESTSRelative to the reference method, the performance of DL on volumetric quantification was assessed using Dice coefficient with 95% confidence interval (CI) for accuracy, two-sided Wilcoxon signed-rank test for computation time, and Bland-Altman analysis on the functional measure derived from the OE images.The DL method produced strong agreement with supervised region growing for the right (Dice: 0.97; 95% CI = [0.96, 0.97]; P < 0.001) and left lungs (Dice: 0.96; 95% CI = [0.96, 0.97]; P < 0.001). The DL method averaged 46 seconds to generate the automatic segmentations in contrast to 1.93 hours using the reference method (P < 0.001). Bland-Altman analysis showed nonsignificant intermethod differences of volumetric (P ≥ 0.12) and functional measurements (P ≥ 0.34) in the left and right lungs.RESULTSThe DL method produced strong agreement with supervised region growing for the right (Dice: 0.97; 95% CI = [0.96, 0.97]; P < 0.001) and left lungs (Dice: 0.96; 95% CI = [0.96, 0.97]; P < 0.001). The DL method averaged 46 seconds to generate the automatic segmentations in contrast to 1.93 hours using the reference method (P < 0.001). Bland-Altman analysis showed nonsignificant intermethod differences of volumetric (P ≥ 0.12) and functional measurements (P ≥ 0.34) in the left and right lungs.DL provides rapid, automated, and robust lung segmentation for quantification of regional lung function using UTE proton MRI.DATA CONCLUSIONDL provides rapid, automated, and robust lung segmentation for quantification of regional lung function using UTE proton MRI.2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;50:1169-1181.LEVEL OF EVIDENCE2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;50:1169-1181.
Author Fain, Sean B.
Schiebler, Mark L.
Nagle, Scott K.
Liu, Fang
Zha, Wei
Evans, Michael D.
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Keywords lung
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cystic fibrosis
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Snippet Background Ultrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development...
Ultrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development of rapid...
BackgroundUltrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development...
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StartPage 1169
SubjectTerms Adult
Artificial neural networks
Asthma
Asthma - diagnostic imaging
Asthma - physiopathology
Automation
Biomarkers
Coders
Confidence intervals
Cystic fibrosis
Cystic Fibrosis - diagnostic imaging
Cystic Fibrosis - physiopathology
deep learning
Female
Field strength
Humans
hyperoxia
Image Interpretation, Computer-Assisted - methods
Image processing
Image segmentation
Imaging, Three-Dimensional - methods
lung
Lung - diagnostic imaging
Lung - physiopathology
Lungs
Machine learning
Magnetic resonance imaging
Magnetic Resonance Imaging - methods
Male
Medical imaging
Neural networks
Neural Networks, Computer
Protons
Rank tests
Regional development
Respiratory function
Retrospective Studies
Statistical analysis
Statistical tests
Structure-function relationships
Title Deep convolutional neural networks with multiplane consensus labeling for lung function quantification using UTE proton MRI
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fjmri.26734
https://www.ncbi.nlm.nih.gov/pubmed/30945385
https://www.proquest.com/docview/2291157933
https://www.proquest.com/docview/2203136607
Volume 50
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