Deep Generative Medical Image Harmonization for Improving Cross‐Site Generalization in Deep Learning Predictors

Background In the medical imaging domain, deep learning‐based methods have yet to see widespread clinical adoption, in part due to limited generalization performance across different imaging devices and acquisition protocols. The deviation between estimated brain age and biological age is an establi...

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Published inJournal of magnetic resonance imaging Vol. 55; no. 3; pp. 908 - 916
Main Authors Bashyam, Vishnu M., Doshi, Jimit, Erus, Guray, Srinivasan, Dhivya, Abdulkadir, Ahmed, Singh, Ashish, Habes, Mohamad, Fan, Yong, Masters, Colin L., Maruff, Paul, Zhuo, Chuanjun, Völzke, Henry, Johnson, Sterling C., Fripp, Jurgen, Koutsouleris, Nikolaos, Satterthwaite, Theodore D., Wolf, Daniel H., Gur, Raquel E., Gur, Ruben C., Morris, John C., Albert, Marilyn S., Grabe, Hans J., Resnick, Susan M., Bryan, Nick R., Wittfeld, Katharina, Bülow, Robin, Wolk, David A., Shou, Haochang, Nasrallah, Ilya M., Davatzikos, Christos
Format Journal Article
LanguageEnglish
Published Hoboken, USA John Wiley & Sons, Inc 01.03.2022
Wiley Subscription Services, Inc
Subjects
Online AccessGet full text
ISSN1053-1807
1522-2586
1522-2586
DOI10.1002/jmri.27908

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Abstract Background In the medical imaging domain, deep learning‐based methods have yet to see widespread clinical adoption, in part due to limited generalization performance across different imaging devices and acquisition protocols. The deviation between estimated brain age and biological age is an established biomarker of brain health and such models may benefit from increased cross‐site generalizability. Purpose To develop and evaluate a deep learning‐based image harmonization method to improve cross‐site generalizability of deep learning age prediction. Study Type Retrospective. Population Eight thousand eight hundred and seventy‐six subjects from six sites. Harmonization models were trained using all subjects. Age prediction models were trained using 2739 subjects from a single site and tested using the remaining 6137 subjects from various other sites. Field Strength/Sequence Brain imaging with magnetization prepared rapid acquisition with gradient echo or spoiled gradient echo sequences at 1.5 T and 3 T. Assessment StarGAN v2, was used to perform a canonical mapping from diverse datasets to a reference domain to reduce site‐based variation while preserving semantic information. Generalization performance of deep learning age prediction was evaluated using harmonized, histogram matched, and unharmonized data. Statistical Tests Mean absolute error (MAE) and Pearson correlation between estimated age and biological age quantified the performance of the age prediction model. Results Our results indicated a substantial improvement in age prediction in out‐of‐sample data, with the overall MAE improving from 15.81 (±0.21) years to 11.86 (±0.11) with histogram matching to 7.21 (±0.22) years with generative adversarial network (GAN)‐based harmonization. In the multisite case, across the 5 out‐of‐sample sites, MAE improved from 9.78 (±6.69) years to 7.74 (±3.03) years with histogram normalization to 5.32 (±4.07) years with GAN‐based harmonization. Data Conclusion While further research is needed, GAN‐based medical image harmonization appears to be a promising tool for improving cross‐site deep learning generalization. Level of Evidence 4 Technical Efficacy Stage 1
AbstractList BackgroundIn the medical imaging domain, deep learning‐based methods have yet to see widespread clinical adoption, in part due to limited generalization performance across different imaging devices and acquisition protocols. The deviation between estimated brain age and biological age is an established biomarker of brain health and such models may benefit from increased cross‐site generalizability.PurposeTo develop and evaluate a deep learning‐based image harmonization method to improve cross‐site generalizability of deep learning age prediction.Study TypeRetrospective.PopulationEight thousand eight hundred and seventy‐six subjects from six sites. Harmonization models were trained using all subjects. Age prediction models were trained using 2739 subjects from a single site and tested using the remaining 6137 subjects from various other sites.Field Strength/SequenceBrain imaging with magnetization prepared rapid acquisition with gradient echo or spoiled gradient echo sequences at 1.5 T and 3 T.AssessmentStarGAN v2, was used to perform a canonical mapping from diverse datasets to a reference domain to reduce site‐based variation while preserving semantic information. Generalization performance of deep learning age prediction was evaluated using harmonized, histogram matched, and unharmonized data.Statistical TestsMean absolute error (MAE) and Pearson correlation between estimated age and biological age quantified the performance of the age prediction model.ResultsOur results indicated a substantial improvement in age prediction in out‐of‐sample data, with the overall MAE improving from 15.81 (±0.21) years to 11.86 (±0.11) with histogram matching to 7.21 (±0.22) years with generative adversarial network (GAN)‐based harmonization. In the multisite case, across the 5 out‐of‐sample sites, MAE improved from 9.78 (±6.69) years to 7.74 (±3.03) years with histogram normalization to 5.32 (±4.07) years with GAN‐based harmonization.Data ConclusionWhile further research is needed, GAN‐based medical image harmonization appears to be a promising tool for improving cross‐site deep learning generalization.Level of Evidence4Technical EfficacyStage 1
Background In the medical imaging domain, deep learning‐based methods have yet to see widespread clinical adoption, in part due to limited generalization performance across different imaging devices and acquisition protocols. The deviation between estimated brain age and biological age is an established biomarker of brain health and such models may benefit from increased cross‐site generalizability. Purpose To develop and evaluate a deep learning‐based image harmonization method to improve cross‐site generalizability of deep learning age prediction. Study Type Retrospective. Population Eight thousand eight hundred and seventy‐six subjects from six sites. Harmonization models were trained using all subjects. Age prediction models were trained using 2739 subjects from a single site and tested using the remaining 6137 subjects from various other sites. Field Strength/Sequence Brain imaging with magnetization prepared rapid acquisition with gradient echo or spoiled gradient echo sequences at 1.5 T and 3 T. Assessment StarGAN v2, was used to perform a canonical mapping from diverse datasets to a reference domain to reduce site‐based variation while preserving semantic information. Generalization performance of deep learning age prediction was evaluated using harmonized, histogram matched, and unharmonized data. Statistical Tests Mean absolute error (MAE) and Pearson correlation between estimated age and biological age quantified the performance of the age prediction model. Results Our results indicated a substantial improvement in age prediction in out‐of‐sample data, with the overall MAE improving from 15.81 (±0.21) years to 11.86 (±0.11) with histogram matching to 7.21 (±0.22) years with generative adversarial network (GAN)‐based harmonization. In the multisite case, across the 5 out‐of‐sample sites, MAE improved from 9.78 (±6.69) years to 7.74 (±3.03) years with histogram normalization to 5.32 (±4.07) years with GAN‐based harmonization. Data Conclusion While further research is needed, GAN‐based medical image harmonization appears to be a promising tool for improving cross‐site deep learning generalization. Level of Evidence 4 Technical Efficacy Stage 1
In the medical imaging domain, deep learning-based methods have yet to see widespread clinical adoption, in part due to limited generalization performance across different imaging devices and acquisition protocols. The deviation between estimated brain age and biological age is an established biomarker of brain health and such models may benefit from increased cross-site generalizability. To develop and evaluate a deep learning-based image harmonization method to improve cross-site generalizability of deep learning age prediction. Retrospective. Eight thousand eight hundred and seventy-six subjects from six sites. Harmonization models were trained using all subjects. Age prediction models were trained using 2739 subjects from a single site and tested using the remaining 6137 subjects from various other sites. Brain imaging with magnetization prepared rapid acquisition with gradient echo or spoiled gradient echo sequences at 1.5 T and 3 T. StarGAN v2, was used to perform a canonical mapping from diverse datasets to a reference domain to reduce site-based variation while preserving semantic information. Generalization performance of deep learning age prediction was evaluated using harmonized, histogram matched, and unharmonized data. Mean absolute error (MAE) and Pearson correlation between estimated age and biological age quantified the performance of the age prediction model. Our results indicated a substantial improvement in age prediction in out-of-sample data, with the overall MAE improving from 15.81 (±0.21) years to 11.86 (±0.11) with histogram matching to 7.21 (±0.22) years with generative adversarial network (GAN)-based harmonization. In the multisite case, across the 5 out-of-sample sites, MAE improved from 9.78 (±6.69) years to 7.74 (±3.03) years with histogram normalization to 5.32 (±4.07) years with GAN-based harmonization. While further research is needed, GAN-based medical image harmonization appears to be a promising tool for improving cross-site deep learning generalization. 4 TECHNICAL EFFICACY: Stage 1.
In the medical imaging domain, deep learning-based methods have yet to see widespread clinical adoption, in part due to limited generalization performance across different imaging devices and acquisition protocols. The deviation between estimated brain age and biological age is an established biomarker of brain health and such models may benefit from increased cross-site generalizability.BACKGROUNDIn the medical imaging domain, deep learning-based methods have yet to see widespread clinical adoption, in part due to limited generalization performance across different imaging devices and acquisition protocols. The deviation between estimated brain age and biological age is an established biomarker of brain health and such models may benefit from increased cross-site generalizability.To develop and evaluate a deep learning-based image harmonization method to improve cross-site generalizability of deep learning age prediction.PURPOSETo develop and evaluate a deep learning-based image harmonization method to improve cross-site generalizability of deep learning age prediction.Retrospective.STUDY TYPERetrospective.Eight thousand eight hundred and seventy-six subjects from six sites. Harmonization models were trained using all subjects. Age prediction models were trained using 2739 subjects from a single site and tested using the remaining 6137 subjects from various other sites.POPULATIONEight thousand eight hundred and seventy-six subjects from six sites. Harmonization models were trained using all subjects. Age prediction models were trained using 2739 subjects from a single site and tested using the remaining 6137 subjects from various other sites.Brain imaging with magnetization prepared rapid acquisition with gradient echo or spoiled gradient echo sequences at 1.5 T and 3 T.FIELD STRENGTH/SEQUENCEBrain imaging with magnetization prepared rapid acquisition with gradient echo or spoiled gradient echo sequences at 1.5 T and 3 T.StarGAN v2, was used to perform a canonical mapping from diverse datasets to a reference domain to reduce site-based variation while preserving semantic information. Generalization performance of deep learning age prediction was evaluated using harmonized, histogram matched, and unharmonized data.ASSESSMENTStarGAN v2, was used to perform a canonical mapping from diverse datasets to a reference domain to reduce site-based variation while preserving semantic information. Generalization performance of deep learning age prediction was evaluated using harmonized, histogram matched, and unharmonized data.Mean absolute error (MAE) and Pearson correlation between estimated age and biological age quantified the performance of the age prediction model.STATISTICAL TESTSMean absolute error (MAE) and Pearson correlation between estimated age and biological age quantified the performance of the age prediction model.Our results indicated a substantial improvement in age prediction in out-of-sample data, with the overall MAE improving from 15.81 (±0.21) years to 11.86 (±0.11) with histogram matching to 7.21 (±0.22) years with generative adversarial network (GAN)-based harmonization. In the multisite case, across the 5 out-of-sample sites, MAE improved from 9.78 (±6.69) years to 7.74 (±3.03) years with histogram normalization to 5.32 (±4.07) years with GAN-based harmonization.RESULTSOur results indicated a substantial improvement in age prediction in out-of-sample data, with the overall MAE improving from 15.81 (±0.21) years to 11.86 (±0.11) with histogram matching to 7.21 (±0.22) years with generative adversarial network (GAN)-based harmonization. In the multisite case, across the 5 out-of-sample sites, MAE improved from 9.78 (±6.69) years to 7.74 (±3.03) years with histogram normalization to 5.32 (±4.07) years with GAN-based harmonization.While further research is needed, GAN-based medical image harmonization appears to be a promising tool for improving cross-site deep learning generalization.DATA CONCLUSIONWhile further research is needed, GAN-based medical image harmonization appears to be a promising tool for improving cross-site deep learning generalization.4 TECHNICAL EFFICACY: Stage 1.LEVEL OF EVIDENCE4 TECHNICAL EFFICACY: Stage 1.
Author Völzke, Henry
Wolk, David A.
Abdulkadir, Ahmed
Fripp, Jurgen
Erus, Guray
Satterthwaite, Theodore D.
Maruff, Paul
Nasrallah, Ilya M.
Resnick, Susan M.
Singh, Ashish
Albert, Marilyn S.
Shou, Haochang
Gur, Ruben C.
Bülow, Robin
Koutsouleris, Nikolaos
Srinivasan, Dhivya
Wolf, Daniel H.
Zhuo, Chuanjun
Masters, Colin L.
Doshi, Jimit
Fan, Yong
Davatzikos, Christos
Bashyam, Vishnu M.
Habes, Mohamad
Johnson, Sterling C.
Morris, John C.
Gur, Raquel E.
Grabe, Hans J.
Bryan, Nick R.
Wittfeld, Katharina
AuthorAffiliation 7 German Centre for Cardiovascular Research, Partner Site Greifswald, Germany
10 Department of Psychiatry and Psychotherapy, Ludwig Maximilian University of Munich
9 CSIRO Health and Biosecurity, Australian e-Health Research Centre CSIRO
13 Department of Neurology, Washington University in St. Louis
17 Laboratory of Behavioral Neuroscience, National Institute on Aging
11 Department of Psychiatry, University of Pennsylvania
1 Artificial Intelligence in Biomedical Imaging Lab, University of Pennsylvania, Philadelphia, PA, USA
2 Biggs Alzheimer’s Institute, University of Texas San Antonio Health Science Center, USA
3 Florey Institute of Neuroscience and Mental Health, University of Melbourne
19 Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Germany
4 Tianjin Mental Health Center, Nankai University Affiliated Tianjin Anding Hospital, Tianjin, China
8 Wisconsin Alzheimer’s Institute, University of Wisconsin School of Medicine and Public Health
6 Institute for Comm
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Copyright 2021 International Society for Magnetic Resonance in Medicine.
2022 International Society for Magnetic Resonance in Medicine
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harmonization
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Snippet Background In the medical imaging domain, deep learning‐based methods have yet to see widespread clinical adoption, in part due to limited generalization...
In the medical imaging domain, deep learning-based methods have yet to see widespread clinical adoption, in part due to limited generalization performance...
BackgroundIn the medical imaging domain, deep learning‐based methods have yet to see widespread clinical adoption, in part due to limited generalization...
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StartPage 908
SubjectTerms Adolescent
Age
Biomarkers
Brain
Brain - diagnostic imaging
Deep Learning
Domains
Field strength
Generative adversarial networks
harmonization
Histograms
Humans
Image Processing, Computer-Assisted - methods
Magnetic resonance imaging
Medical imaging
Medical research
Neuroimaging
Population studies
Prediction models
Research Design
Retrospective Studies
StarGAN
Statistical analysis
Statistical tests
Title Deep Generative Medical Image Harmonization for Improving Cross‐Site Generalization in Deep Learning Predictors
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fjmri.27908
https://www.ncbi.nlm.nih.gov/pubmed/34564904
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https://pubmed.ncbi.nlm.nih.gov/PMC8844038
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