2020
Multi-site fMRI analysis using privacy-preserving federated learning and domain adaptation: ABIDE results
Li X, Gu Y, Dvornek N, Staib LH, Ventola P, Duncan JS. Multi-site fMRI analysis using privacy-preserving federated learning and domain adaptation: ABIDE results. Medical Image Analysis 2020, 65: 101765. PMID: 32679533, PMCID: PMC7569477, DOI: 10.1016/j.media.2020.101765.Peer-Reviewed Original ResearchConceptsDeep learning modelsFederated LearningPrivacy-preserving federated learningLearning modelFederated learning approachPrivacy-preserving strategyDomain adaptation methodsData analysis problemsLocal model weightsIterative optimization algorithmEntity dataDomain adaptationLearning approachLearning formulationMulti-site dataRandomization mechanismAdaptation methodNeuroimage analysisDifferent tasksModel weightsModel optimizationOptimization algorithmPrivate informationTraining strategyAnalysis problemSparse 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 Research
2017
Learning Non-rigid Deformations for Robust, Constrained Point-based Registration in Image-Guided MR-TRUS Prostate Intervention
Onofrey JA, Staib LH, Sarkar S, Venkataraman R, Nawaf CB, Sprenkle PC, Papademetris X. Learning Non-rigid Deformations for Robust, Constrained Point-based Registration in Image-Guided MR-TRUS Prostate Intervention. Medical Image Analysis 2017, 39: 29-43. PMID: 28431275, PMCID: PMC5514316, DOI: 10.1016/j.media.2017.04.001.Peer-Reviewed Original Research
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 ResearchSegmenting the Brain Surface from CT Images with Artifacts Using Dictionary Learning for Non-rigid MR-CT Registration
Onofrey JA, Staib LH, Papademetris X. Segmenting the Brain Surface from CT Images with Artifacts Using Dictionary Learning for Non-rigid MR-CT Registration. Lecture Notes In Computer Science 2015, 24: 662-674. PMID: 26221711, PMCID: PMC5266617, DOI: 10.1007/978-3-319-19992-4_52.Peer-Reviewed Original Research
2014
Radial Basis Functions for Combining Shape and Speckle Tracking in 4D Echocardiography
Compas C, Wong EY, Huang X, Sampath S, Lin BA, Pal P, Papademetris X, Thiele K, Dione DP, Stacy M, Staib LH, Sinusas AJ, O'Donnell M, Duncan JS. Radial Basis Functions for Combining Shape and Speckle Tracking in 4D Echocardiography. IEEE Transactions On Medical Imaging 2014, 33: 1275-1289. PMID: 24893257, PMCID: PMC4283552, DOI: 10.1109/tmi.2014.2308894.Peer-Reviewed Original Research
2013
Contour tracking in echocardiographic sequences via sparse representation and dictionary learning
Huang X, Dione DP, Compas CB, Papademetris X, Lin BA, Bregasi A, Sinusas AJ, Staib LH, Duncan JS. Contour tracking in echocardiographic sequences via sparse representation and dictionary learning. Medical Image Analysis 2013, 18: 253-271. PMID: 24292554, PMCID: PMC3946038, DOI: 10.1016/j.media.2013.10.012.Peer-Reviewed Original ResearchConceptsContour trackerSparse representationEchocardiographic sequencesRegion-based level set segmentationLevel set segmentationLocal image appearanceManual tracingExpert manual tracingsMultiscale sparse representationImage sequencesSegmentation resultsAppearance modelSpatiotemporal priorsFirst frameMultilevel informationHuman data setsEjection fraction estimatesLocal appearanceImage appearanceDictionary learningShape modelContour trackingManual resultsData setsContour estimationLearning Nonrigid Deformations for Constrained Multi-modal Image Registration
Onofrey JA, Staib LH, Papademetris X. Learning Nonrigid Deformations for Constrained Multi-modal Image Registration. Lecture Notes In Computer Science 2013, 16: 171-178. PMID: 24505758, PMCID: PMC4044829, DOI: 10.1007/978-3-642-40760-4_22.Peer-Reviewed Original Research
2012
Anatomical Brain Images Alone Can Accurately Diagnose Chronic Neuropsychiatric Illnesses
Bansal R, Staib LH, Laine AF, Hao X, Xu D, Liu J, Weissman M, Peterson BS. Anatomical Brain Images Alone Can Accurately Diagnose Chronic Neuropsychiatric Illnesses. PLOS ONE 2012, 7: e50698. PMID: 23236384, PMCID: PMC3517530, DOI: 10.1371/journal.pone.0050698.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAlgorithmsAttention Deficit Disorder with HyperactivityBipolar DisorderBrainChildDepressive Disorder, MajorFemaleHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMaleMiddle AgedReproducibility of ResultsSchizophreniaSensitivity and SpecificityTourette SyndromeConceptsBrains of personsNeuropsychiatric illnessBrain regionsNeuropsychiatric disordersMRI scansMajor depressive disorderChronic neuropsychiatric disorderAttention-deficit/hyperactivity disorderSpecific neuropsychiatric disordersDifferent neuropsychiatric disordersLarge MRI datasetsAnatomical MRI scansDisease courseCerebral cortexLow familial riskDepressive disorderBiological subtypesTourette syndromeBipolar disorderAnatomical brain imagesClinical diagnosisFamilial riskIllnessDiagnostic accuracyDiagnostic algorithmVolumetric Intraoperative Brain Deformation Compensation: Model Development and Phantom Validation
DeLorenzo C, Papademetris X, Staib LH, Vives KP, Spencer DD, Duncan JS. Volumetric Intraoperative Brain Deformation Compensation: Model Development and Phantom Validation. IEEE Transactions On Medical Imaging 2012, 31: 1607-1619. PMID: 22562728, PMCID: PMC3600363, DOI: 10.1109/tmi.2012.2197407.Peer-Reviewed Original ResearchConceptsLinear elastic modelSurface displacementsElastic modelBrain deformationVolumetric brain deformationMaterial parametersMaterial propertiesRealistic brain phantomDeformationBiomechanical modelIntraoperative brainModel accuracyLocalization errorPhantom validationAccurate surgical guidanceModel solutionsModel developmentInitial estimationDisplacementModel sensitivityQuantitative validationPhantom resultsPreoperative imagesSurgical guidancePreliminary applicationSimultaneous Nonrigid Registration, Segmentation, and Tumor Detection in MRI Guided Cervical Cancer Radiation Therapy
Lu C, Chelikani S, Jaffray DA, Milosevic MF, Staib LH, Duncan JS. Simultaneous Nonrigid Registration, Segmentation, and Tumor Detection in MRI Guided Cervical Cancer Radiation Therapy. IEEE Transactions On Medical Imaging 2012, 31: 1213-1227. PMID: 22328178, PMCID: PMC3889159, DOI: 10.1109/tmi.2012.2186976.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsFemaleHumansImage EnhancementImage Interpretation, Computer-AssistedImaging, Three-DimensionalMagnetic Resonance ImagingPattern Recognition, AutomatedRadiotherapy, ConformalRadiotherapy, Image-GuidedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueUterine Cervical Neoplasms
2011
Fasciculography: Robust Prior-Free Real-Time Normalized Volumetric Neural Tract Parcellation
Ho P, Wang F, Papademetris X, Blumberg HP, Staib LH. Fasciculography: Robust Prior-Free Real-Time Normalized Volumetric Neural Tract Parcellation. IEEE Transactions On Medical Imaging 2011, 31: 217-230. PMID: 21914568, PMCID: PMC3640528, DOI: 10.1109/tmi.2011.2167629.Peer-Reviewed Original ResearchConceptsDiffusion tensor magnetic resonance imagesLess human interventionSearch spaceAbnormality detectionHuman interventionDiffusion tensor fieldsAbove problemsOrientation informationNonrigid registrationIncomplete reconstructionStreamline trackingTrackingOrientation errorsMagnetic resonance imagesImage artifactsTracking errorFiber trackingWhite matter fiber tractsLocal noiseTensor fieldsResonance imagesParcellation methodSame timeInitializationViable toolAn integrated approach to segmentation and nonrigid registration for application in image-guided pelvic radiotherapy
Lu C, Chelikani S, Papademetris X, Knisely JP, Milosevic MF, Chen Z, Jaffray DA, Staib LH, Duncan JS. An integrated approach to segmentation and nonrigid registration for application in image-guided pelvic radiotherapy. Medical Image Analysis 2011, 15: 772-785. PMID: 21646038, PMCID: PMC3164526, DOI: 10.1016/j.media.2011.05.010.Peer-Reviewed Original ResearchAlgorithmsBayes TheoremFemaleHumansImaging, Three-DimensionalMaleProstatic NeoplasmsRadiographic Image EnhancementRadiographic Image Interpretation, Computer-AssistedRadiotherapy, Computer-AssistedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueSystems IntegrationTomography, X-Ray ComputedUterine Cervical NeoplasmsUnified Framework for Development, Deployment and Robust Testing of Neuroimaging Algorithms
Joshi A, Scheinost D, Okuda H, Belhachemi D, Murphy I, Staib LH, Papademetris X. Unified Framework for Development, Deployment and Robust Testing of Neuroimaging Algorithms. Neuroinformatics 2011, 9: 69-84. PMID: 21249532, PMCID: PMC3066099, DOI: 10.1007/s12021-010-9092-8.Peer-Reviewed Original ResearchConceptsUser interface controlsUser interfaceNovel object-oriented frameworkCommand-line user interfaceGraphical user interface controlsMedical image analysisObject-oriented frameworkComplex image analysisImage analysisPlatform interoperabilitySoftware objectsReusable componentsInterface controlSource codeSuch algorithmsFramework idealMultiple platformsUnified frameworkAlgorithmRapid developmentDeploymentThorough testingPublic useFrameworkPlatformIntegrated Parcellation and Normalization Using DTI Fasciculography
Ho HP, Wang F, Papademetris X, Blumberg HP, Staib LH. Integrated Parcellation and Normalization Using DTI Fasciculography. Lecture Notes In Computer Science 2011, 14: 33-41. PMID: 21995010, PMCID: PMC3701295, DOI: 10.1007/978-3-642-23629-7_5.Peer-Reviewed Original ResearchConceptsDiffusion magnetic resonance imagesExtensive human interventionCumulative tracking errorsInteractive speedHuman interventionOrientation informationImage noiseMagnetic resonance imagesTracking errorVirtual pathwaysNormalization methodImagesDiffusion imagesWhite matter fasciclesFiber trackingCross-subject statisticsResonance imagesNew techniqueTrackingErrorVisualizationImplementationConnectivityInformationParcellationVessel Connectivity Using Murray’s Hypothesis
Jiang Y, Zhuang ZW, Sinusas AJ, Staib LH, Papademetris X. Vessel Connectivity Using Murray’s Hypothesis. Lecture Notes In Computer Science 2011, 14: 528-536. PMID: 22003740, PMCID: PMC3367766, DOI: 10.1007/978-3-642-23626-6_65.Peer-Reviewed Original Research
2010
Refraction corrected transmission ultrasound computed tomography for application in breast imaging
Li S, Jackowski M, Dione DP, Varslot T, Staib LH, Mueller K. Refraction corrected transmission ultrasound computed tomography for application in breast imaging. Medical Physics 2010, 37: 2233-2246. PMID: 20527557, PMCID: PMC2874040, DOI: 10.1118/1.3360180.Peer-Reviewed Original ResearchImage-Guided Intraoperative Cortical Deformation Recovery Using Game Theory: Application to Neocortical Epilepsy Surgery
DeLorenzo C, Papademetris X, Staib LH, Vives KP, Spencer DD, Duncan JS. Image-Guided Intraoperative Cortical Deformation Recovery Using Game Theory: Application to Neocortical Epilepsy Surgery. IEEE Transactions On Medical Imaging 2010, 29: 322-338. PMID: 20129844, PMCID: PMC2824434, DOI: 10.1109/tmi.2009.2027993.Peer-Reviewed Original ResearchConceptsDeformation estimationSurface deformationBrain surface deformationSurface deformation estimationPreoperative brain imagesCortical surface deformationSurface trackingCamera calibration parametersDisplacement errorStereo vision systemBrain deformationDeformationCalibration parametersBiomechanical modelIntraoperative brainCalibration errorsPhysical processesVision systemVivo casesCamera calibrationStereo systemInitial conditionsImage acquisitionErrorEstimationIntegrated Segmentation and Nonrigid Registration for Application in Prostate Image-Guided Radiotherapy
Lu C, Chelikani S, Chen Z, Papademetris X, Staib LH, Duncan JS. Integrated Segmentation and Nonrigid Registration for Application in Prostate Image-Guided Radiotherapy. Lecture Notes In Computer Science 2010, 13: 53-60. PMID: 20879214, DOI: 10.1007/978-3-642-15705-9_7.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsHumansImaging, Three-DimensionalMaleProstatic NeoplasmsRadiographic Image EnhancementRadiographic Image Interpretation, Computer-AssistedRadiotherapy, Computer-AssistedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueSystems IntegrationTomography, X-Ray ComputedConceptsManual segmentationAutomatic segmentationImportant treatment parametersNonrigid registrationImage-guided radiotherapy systemReal patient dataNon-rigid registrationIntegrated SegmentationRegistration partRadiotherapy linear acceleratorSegmentationTreatment imagesImage qualityCone-beam CTTreatment parametersImagesPromising resultsPatient dataKey anatomical structuresLinear acceleratorRegistrationPrevious workRadiotherapy system
2009
Constrained non-rigid registration for use in image-guided adaptive radiotherapy
Greene WH, Chelikani S, Purushothaman K, Knisely JP, Chen Z, Papademetris X, Staib LH, Duncan JS. Constrained non-rigid registration for use in image-guided adaptive radiotherapy. Medical Image Analysis 2009, 13: 809-817. PMID: 19682945, PMCID: PMC2771756, DOI: 10.1016/j.media.2009.07.004.Peer-Reviewed Original ResearchAlgorithmsArtificial IntelligenceHumansMalePattern Recognition, AutomatedProstatic NeoplasmsRadiographic Image EnhancementRadiographic Image Interpretation, Computer-AssistedRadiotherapy, Computer-AssistedRadiotherapy, ConformalReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueTomography, X-Ray Computed