2023
DuSFE: Dual-Channel Squeeze-Fusion-Excitation co-attention for cross-modality registration of cardiac SPECT and CT
Chen X, Zhou B, Xie H, Guo X, Zhang J, Duncan J, Miller E, Sinusas A, Onofrey J, Liu C. DuSFE: Dual-Channel Squeeze-Fusion-Excitation co-attention for cross-modality registration of cardiac SPECT and CT. Medical Image Analysis 2023, 88: 102840. PMID: 37216735, PMCID: PMC10524650, DOI: 10.1016/j.media.2023.102840.Peer-Reviewed Original ResearchMeSH KeywordsHeartHumansImage Processing, Computer-AssistedPhantoms, ImagingTomography, Emission-Computed, Single-PhotonTomography, X-Ray ComputedConceptsCross-modality registrationConvolutional layersCo-attention mechanismMultiple convolutional layersCo-attention moduleDifferent convolutional layersMedical image registrationInput data streamDeep learning strategiesLow registration errorIntensity-based registration methodCardiac SPECTΜ-mapsDeep learningFeature fusionData streamsInput imageSource codeFeature mapsNeural networkImage registrationSpatial featuresRegistration performanceRegistration methodInput informationDeep learning-based attenuation map generation with simultaneously reconstructed PET activity and attenuation and low-dose application
Shi L, Zhang J, Toyonaga T, Shao D, Onofrey J, Lu Y. Deep learning-based attenuation map generation with simultaneously reconstructed PET activity and attenuation and low-dose application. Physics In Medicine And Biology 2023, 68: 035014. PMID: 36584395, DOI: 10.1088/1361-6560/acaf49.Peer-Reviewed Original Research
2022
An objective evaluation method for head motion estimation in PET—Motion corrected centroid-of-distribution
Sun C, Revilla EM, Zhang J, Fontaine K, Toyonaga T, Gallezot JD, Mulnix T, Onofrey JA, Carson RE, Lu Y. An objective evaluation method for head motion estimation in PET—Motion corrected centroid-of-distribution. NeuroImage 2022, 264: 119678. PMID: 36261057, DOI: 10.1016/j.neuroimage.2022.119678.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBrainHumansImage Processing, Computer-AssistedMotionPositron-Emission TomographyConceptsMotion informationHardware-based methodsHead motion estimationPET image reconstructionMotion estimation methodData-driven methodPET raw dataHead motionMask segmentationFinal image qualityMotion estimationTracking hardwareDifferent motion estimation methodsBrain PET studiesGround truthImage reconstructionRaw dataNew algorithmObjective quality controlInaccurate motion informationImage qualityMotion correction algorithmAlgorithmMotion errorsCorrection algorithm
2020
Deep learning-based attenuation map generation for myocardial perfusion SPECT
Shi L, Onofrey JA, Liu H, Liu YH, Liu C. Deep learning-based attenuation map generation for myocardial perfusion SPECT. European Journal Of Nuclear Medicine And Molecular Imaging 2020, 47: 2383-2395. PMID: 32219492, DOI: 10.1007/s00259-020-04746-6.Peer-Reviewed Original ResearchMeSH KeywordsArtifactsDeep LearningHumansImage Processing, Computer-AssistedPerfusionTomography, Emission-Computed, Single-PhotonTomography, X-Ray ComputedSparse Data–Driven Learning for Effective and Efficient Biomedical Image Segmentation
Onofrey JA, Staib LH, Huang X, Zhang F, Papademetris X, Metaxas D, Rueckert D, Duncan JS. Sparse Data–Driven Learning for Effective and Efficient Biomedical Image Segmentation. Annual Review Of Biomedical Engineering 2020, 22: 1-27. PMID: 32169002, PMCID: PMC9351438, DOI: 10.1146/annurev-bioeng-060418-052147.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBrainDeep LearningDogsEchocardiographyHeart VentriclesHumansImage Processing, Computer-AssistedImaging, Three-DimensionalMachine LearningModels, TheoreticalNeural Networks, ComputerTomography, X-Ray Computed
2019
An investigation of quantitative accuracy for deep learning based denoising in oncological PET
Lu W, Onofrey JA, Lu Y, Shi L, Ma T, Liu Y, Liu C. An investigation of quantitative accuracy for deep learning based denoising in oncological PET. Physics In Medicine And Biology 2019, 64: 165019. PMID: 31307019, DOI: 10.1088/1361-6560/ab3242.Peer-Reviewed Original ResearchAlgorithmsDeep LearningHumansImage EnhancementImage Processing, Computer-AssistedNeoplasmsNormal DistributionPositron-Emission TomographySignal-To-Noise RatioData-driven voluntary body motion detection and non-rigid event-by-event correction for static and dynamic PET
Lu Y, Gallezot JD, Naganawa M, Ren S, Fontaine K, Wu J, Onofrey JA, Toyonaga T, Boutagy N, Mulnix T, Panin VY, Casey ME, Carson RE, Liu C. Data-driven voluntary body motion detection and non-rigid event-by-event correction for static and dynamic PET. Physics In Medicine And Biology 2019, 64: 065002. PMID: 30695768, DOI: 10.1088/1361-6560/ab02c2.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsDogsFluorodeoxyglucose F18HaplorhiniHumansImage Processing, Computer-AssistedMonitoring, PhysiologicMovementOrgan MotionPositron-Emission TomographyRespirationRespiratory-Gated Imaging TechniquesConceptsCentroid of distribution
2018
Deep-learned placental vessel segmentation for intraoperative video enhancement in fetoscopic surgery
Sadda P, Imamoglu M, Dombrowski M, Papademetris X, Bahtiyar MO, Onofrey J. Deep-learned placental vessel segmentation for intraoperative video enhancement in fetoscopic surgery. International Journal Of Computer Assisted Radiology And Surgery 2018, 14: 227-235. PMID: 30484115, PMCID: PMC6438174, DOI: 10.1007/s11548-018-1886-4.Peer-Reviewed Original ResearchMeSH KeywordsDeep LearningFemaleFetofetal TransfusionFetoscopyHumansImage Processing, Computer-AssistedLaser CoagulationPlacentaPregnancySensitivity and SpecificityVascular Surgical ProceduresSegmenting the Brain Surface From CT Images With Artifacts Using Locally Oriented Appearance and Dictionary Learning
Onofrey JA, Staib LH, Papademetris X. Segmenting the Brain Surface From CT Images With Artifacts Using Locally Oriented Appearance and Dictionary Learning. IEEE Transactions On Medical Imaging 2018, 38: 596-607. PMID: 30176584, PMCID: PMC6476428, DOI: 10.1109/tmi.2018.2868045.Peer-Reviewed Original ResearchMeSH KeywordsArtifactsBrainDeep LearningHumansImage Processing, Computer-AssistedSurgery, Computer-AssistedTomography, X-Ray ComputedRespiratory Motion Compensation for PET/CT with Motion Information Derived from Matched Attenuation-Corrected Gated PET Data
Lu Y, Fontaine K, Mulnix T, Onofrey JA, Ren S, Panin V, Jones J, Casey ME, Barnett R, Kench P, Fulton R, Carson RE, Liu C. Respiratory Motion Compensation for PET/CT with Motion Information Derived from Matched Attenuation-Corrected Gated PET Data. Journal Of Nuclear Medicine 2018, 59: 1480-1486. PMID: 29439015, PMCID: PMC6126443, DOI: 10.2967/jnumed.117.203000.Peer-Reviewed Original ResearchMeSH KeywordsArtifactsFour-Dimensional Computed TomographyHumansImage Processing, Computer-AssistedMovementPositron Emission Tomography Computed TomographyRespirationRespiratory-Gated Imaging TechniquesConceptsMotion correction frameworkMotion informationReference gatePET reconstructionMotion estimation accuracyGated PET dataMotion compensation approachMotion correctionMotion compensation methodMotion estimationRespiratory motion compensationAttenuation correction artifactsLung cancer datasetMotion compensationCT imagesNAC approachReconstruction algorithmPET dataPET imagesNew frameworkInaccurate localizationCancer datasetsBreathing variationsAttenuation correction mapsHuman datasets
2017
Non-Rigid Event-by-Event Continuous Respiratory Motion Compensated List-Mode Reconstruction for PET
Chan C, Onofrey J, Jian Y, Germino M, Papademetris X, Carson RE, Liu C. Non-Rigid Event-by-Event Continuous Respiratory Motion Compensated List-Mode Reconstruction for PET. IEEE Transactions On Medical Imaging 2017, 37: 504-515. PMID: 29028189, PMCID: PMC7304524, DOI: 10.1109/tmi.2017.2761756.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsFluorodeoxyglucose F18HumansImage Processing, Computer-AssistedPhantoms, ImagingPositron Emission Tomography Computed TomographyRespiratory MechanicsConceptsMotion-compensated image reconstructionMotion fieldImage reconstructionReconstruction algorithmRespiratory motionNon-rigid motionNon-rigid motion correctionSignificant image blurringSystem matrixMotion correctionSystem matrix calculationMotionImage blurringSuperior image qualityTracer concentrationRigid motionReference locationMatrix calculationList-mode reconstruction algorithmMotion correlationDynamics studyImage quality
2015
Learning intervention-induced deformations for non-rigid MR-CT registration and electrode localization in epilepsy patients
Onofrey JA, Staib LH, Papademetris X. Learning intervention-induced deformations for non-rigid MR-CT registration and electrode localization in epilepsy patients. NeuroImage Clinical 2015, 10: 291-301. PMID: 26900569, PMCID: PMC4724039, DOI: 10.1016/j.nicl.2015.12.001.Peer-Reviewed Original Research