2021
BrainGNN: Interpretable Brain Graph Neural Network for fMRI Analysis
Li X, Zhou Y, Dvornek N, Zhang M, Gao S, Zhuang J, Scheinost D, Staib LH, Ventola P, Duncan JS. BrainGNN: Interpretable Brain Graph Neural Network for fMRI Analysis. Medical Image Analysis 2021, 74: 102233. PMID: 34655865, PMCID: PMC9916535, DOI: 10.1016/j.media.2021.102233.Peer-Reviewed Original ResearchConceptsFunctional magnetic resonance imagesGraph neural network frameworkMedical image analysisGraph neural networkGraph convolutional layersNeural network frameworkDifferent evaluation metricsSpecific task statesIndependent fMRI datasetsPooling layerConvolutional layersConsistency lossNetwork frameworkNeural networkFMRI datasetsImage analysis methodEvaluation metricsDetection resultsBrain graphsSubjects releaseROI selectionImage analysisCognitive stimuliTask statesFMRI analysis
2020
Sparse 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
2016
Brain responses to biological motion predict treatment outcome in young children with autism
Yang D, Pelphrey KA, Sukhodolsky DG, Crowley MJ, Dayan E, Dvornek NC, Venkataraman A, Duncan J, Staib L, Ventola P. Brain responses to biological motion predict treatment outcome in young children with autism. Translational Psychiatry 2016, 6: e948-e948. PMID: 27845779, PMCID: PMC5314125, DOI: 10.1038/tp.2016.213.Peer-Reviewed Original ResearchConceptsAutism spectrum disorderYoung childrenSocial information processingMultivariate pattern analysisMotivation/rewardBiological motionCore deficitComplex neurodevelopmental disorderBrain responsesResponse treatmentSpectrum disorderNeurobiological markersNeural predictorsInformation processingBehavioral interventionsIndividual childrenNeurodevelopmental disordersCurrent findingsNeural circuitsBehavioral deficitsEarly childhoodChildrenUnsuccessful interventionsNeurobiomarkersPattern analysisPivotal response treatment prompts a functional rewiring of the brain among individuals with autism spectrum disorder
Venkataraman A, Yang D, Dvornek N, Staib LH, Duncan JS, Pelphrey KA, Ventola P. Pivotal response treatment prompts a functional rewiring of the brain among individuals with autism spectrum disorder. Neuroreport 2016, 27: 1081-1085. PMID: 27532879, PMCID: PMC5007196, DOI: 10.1097/wnr.0000000000000662.Peer-Reviewed Original ResearchConceptsPivotal Response TreatmentAutism spectrum disorderOccipital-temporal cortexAttentional systemResponse treatmentSpectrum disorderOrbitofrontal cortexPosterior cingulateHigh-level objectsBehavioral interventionsLearning mechanismPerception shiftProcessing areasNeural circuitsFunctional rewiringCortexTreatment regimenAutismInterventionNovel Bayesian frameworkCingulateFunctional changesIndividualsDisordersObjects
2012
Volumetric 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 application
2011
Non-rigid Registration of Longitudinal Brain Tumor Treatment MRI
Chitphakdithai N, Chiang VL, Duncan JS. Non-rigid Registration of Longitudinal Brain Tumor Treatment MRI. Annual International Conference Of The IEEE Engineering In Medicine And Biology Society (EMBC) 2011, 2011: 4893-4896. PMID: 22255435, PMCID: PMC3753806, DOI: 10.1109/iembs.2011.6091212.Peer-Reviewed Original Research
2010
Non-rigid Registration with Missing Correspondences in Preoperative and Postresection Brain Images
Chitphakdithai N, Duncan JS. Non-rigid Registration with Missing Correspondences in Preoperative and Postresection Brain Images. Lecture Notes In Computer Science 2010, 13: 367-374. PMID: 20879252, PMCID: PMC3031159, DOI: 10.1007/978-3-642-15705-9_45.Peer-Reviewed Original ResearchConceptsTypes of datasetsNon-rigid registration methodImage alignmentNon-rigid registrationMissing correspondencesSegmentation algorithmNon-rigid registration algorithmSimilarity metricCorrespondence problemValid correspondencesRegistration algorithmRegistration methodExpectation-maximization algorithmBrain imagesJoint registrationReal dataAlgorithmImagesRegistrationError kernel
2008
Bayesian Analysis of fMRI Data with ICA Based Spatial Prior
Bathula DR, Tagare HD, Staib LH, Papademetris X, Schultz RT, Duncan JS. Bayesian Analysis of fMRI Data with ICA Based Spatial Prior. Lecture Notes In Computer Science 2008, 11: 246-254. PMID: 18982612, PMCID: PMC2864117, DOI: 10.1007/978-3-540-85990-1_30.Peer-Reviewed Original Research
2007
A Comprehensive System for Intraoperative 3D Brain Deformation Recovery
DeLorenzo C, Papademetris X, Vives KP, Spencer DD, Duncan JS. A Comprehensive System for Intraoperative 3D Brain Deformation Recovery. Lecture Notes In Computer Science 2007, 10: 553-561. PMID: 18044612, PMCID: PMC2864112, DOI: 10.1007/978-3-540-75759-7_67.Peer-Reviewed Original ResearchConceptsBrain deformationLinear elastic modelVolumetric brain deformationDeformation recoverySurface trackingSurface displacementsElastic modelRealistic brain phantomDeformationBiomechanical modelLarge brain deformationsIntraoperative brainFeature detectionSemiautomatic strategyBrain phantomPreoperative imagesDisplacement
2006
Nonrigid 3D Brain Registration Using Intensity/Feature Information
DeLorenzo C, Papademetris X, Wu K, Vives KP, Spencer D, Duncan JS. Nonrigid 3D Brain Registration Using Intensity/Feature Information. Lecture Notes In Computer Science 2006, 9: 932-939. PMID: 17354980, PMCID: PMC2864121, DOI: 10.1007/11866565_114.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtificial IntelligenceBayes TheoremBrainEpilepsyHumansImage EnhancementImage Interpretation, Computer-AssistedImaging, Three-DimensionalMagnetic Resonance ImagingPattern Recognition, AutomatedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueSurgery, Computer-AssistedConceptsStereo camera imagesCamera calibration errorsPreoperative brain imagesSurface tracking algorithmFeature informationCamera imagesTracking algorithmBrain imagesOptimization termSurface detectionRobust modelImagesBrain registrationIntraoperative brainCalibration errorsAlgorithmAccuracyRegistrationModelInformation
2004
Neighbor-Constrained Segmentation With Level Set Based 3-D Deformable Models
Yang J, Staib LH, Duncan JS. Neighbor-Constrained Segmentation With Level Set Based 3-D Deformable Models. IEEE Transactions On Medical Imaging 2004, 23: 940-948. PMID: 15338728, PMCID: PMC2838450, DOI: 10.1109/tmi.2004.830802.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBrainComputer SimulationElasticityHumansImage EnhancementImage Interpretation, Computer-AssistedImaging, Three-DimensionalInformation Storage and RetrievalMagnetic Resonance ImagingModels, BiologicalModels, StatisticalNumerical Analysis, Computer-AssistedPattern Recognition, AutomatedReproducibility of ResultsSensitivity and SpecificitySignal Processing, Computer-AssistedConceptsThree-dimensional medical imagesImage gray level informationGray level informationPoint distribution modelMedical imagesNeighbor objectsTraining imagesMedical imageryMultiple objectsDeformable modelObject shapeSynthetic dataLevel informationSegmentationMap shapeEstimation frameworkPosition relationshipPrior informationLevel set functionObjectsJoint probability distributionSet functionNeighboring shapesInformationImagesGeometric strategies for neuroanatomic analysis from MRI
Duncan JS, Papademetris X, Yang J, Jackowski M, Zeng X, Staib LH. Geometric strategies for neuroanatomic analysis from MRI. NeuroImage 2004, 23: s34-s45. PMID: 15501099, PMCID: PMC2832750, DOI: 10.1016/j.neuroimage.2004.07.027.Peer-Reviewed Original ResearchConceptsApplied mathematical approachWhite matter fiber tracksStatistical estimationMathematical approachFunction-structure analysisMagnetic resonance imagesEvolution strategyGeometric constraintsImage processingIntersubject registrationRich setGeometric strategyOngoing workData setsUse of levelsCommon spaceNeuroanatomic analysisSetRegistrationFiber tracksHuman brainResonance imagesInformationSegmentationEstimation
2003
A unified non-rigid feature registration method for brain mapping
Chui H, Win L, Schultz R, Duncan JS, Rangarajan A. A unified non-rigid feature registration method for brain mapping. Medical Image Analysis 2003, 7: 113-130. PMID: 12868617, DOI: 10.1016/s1361-8415(02)00102-0.Peer-Reviewed Original ResearchNeighbor-Constrained Segmentation with 3D Deformable Models
Yang J, Staib LH, Duncan JS. Neighbor-Constrained Segmentation with 3D Deformable Models. Lecture Notes In Computer Science 2003, 18: 198-209. PMID: 15344458, DOI: 10.1007/978-3-540-45087-0_17.Peer-Reviewed Original ResearchConceptsImage gray level informationGray level informationNeighbor objectsMedical imagesTraining imagesMedical imageryMultiple objectsDeformable modelSynthetic dataLevel informationSegmentationMap shapeEstimation frameworkPrior informationLevel set functionObjectsJoint probability distributionSet functionInformationImagesNovel methodMaximum AJoint density functionProbability distributionFramework
2002
Model-driven brain shift compensation
Škrinjar O, Nabavi A, Duncan J. Model-driven brain shift compensation. Medical Image Analysis 2002, 6: 361-373. PMID: 12494947, DOI: 10.1016/s1361-8415(02)00062-2.Peer-Reviewed Original ResearchConceptsBrain shift compensationShift compensationIntraoperative surface dataIntraoperative brain deformationSpring-mass modelContinuum mechanicsBrain deformationNavigation systemSame coordinate systemDeformationSurface dataBrain shiftMR image sequencesCoordinate systemImage sequencesSurgical navigation systemDominant errorCompensationPartial validationFull volumeSystemError
1997
Positron Emission Tomography Measurement of Cerebral Metabolic Correlates of Tryptophan Depletion—Induced Depressive Relapse
Bremner JD, Innis RB, Salomon RM, Staib LH, Ng CK, Miller HL, Bronen RA, Krystal JH, Duncan J, Rich D, Price LH, Malison R, Dey H, Soufer R, Charney DS. Positron Emission Tomography Measurement of Cerebral Metabolic Correlates of Tryptophan Depletion—Induced Depressive Relapse. JAMA Psychiatry 1997, 54: 364-374. PMID: 9107153, DOI: 10.1001/archpsyc.1997.01830160092012.Peer-Reviewed Original ResearchConceptsCerebral metabolic correlatesDepressive relapseBrain metabolismMajor depressionMiddle frontal gyrusOrbitofrontal cortexTryptophan depletionMetabolic correlatesPositron emission tomography scanningFrontal gyrusRelapse-prone patientsPathogenesis of depressionPositron emission tomography (PET) measurementsSerotonin reuptake inhibitorsSymptoms of patientsPositron emission tomographySingle photon emissionSpecific brain regionsDorsolateral prefrontal cortexReuptake inhibitorsPlasma tryptophanLimbic regionsCaudate nucleusDepressive symptomsPatientsPositron Emission Tomography Measurement of Cerebral Metabolic Correlates of Yohimbine Administration in Combat-Related Posttraumatic Stress Disorder
Bremner JD, Innis RB, Ng CK, Staib LH, Salomon RM, Bronen RA, Duncan J, Southwick SM, Krystal JH, Rich D, Zubal G, Dey H, Soufer R, Charney DS. Positron Emission Tomography Measurement of Cerebral Metabolic Correlates of Yohimbine Administration in Combat-Related Posttraumatic Stress Disorder. JAMA Psychiatry 1997, 54: 246-254. PMID: 9075465, DOI: 10.1001/archpsyc.1997.01830150070011.Peer-Reviewed Original ResearchConceptsPosttraumatic stress disorderAdministration of yohimbineNorepinephrine releaseHealthy subjectsHealthy age-matched control subjectsAge-matched control subjectsStress disorderDouble-blind fashionPositron emission tomography (PET) measurementsBrain metabolic responsesCerebral metabolic correlatesBrain norepinephrine releaseSymptoms of anxietyPositron emission tomographyBrain metabolismControl subjectsYohimbine administrationPreclinical studiesMetabolic correlatesCaudate nucleusPatientsYohimbineVietnam combat veteransEmission tomographyOrbitofrontal cortex