2023
Learning Sequential Information in Task-Based fMRI for Synthetic Data Augmentation
Wang J, Dvornek N, Staib L, Duncan J. Learning Sequential Information in Task-Based fMRI for Synthetic Data Augmentation. Lecture Notes In Computer Science 2023, 14312: 79-88. PMID: 39281201, PMCID: PMC11395879, DOI: 10.1007/978-3-031-44858-4_8.Peer-Reviewed Original ResearchFunctional magnetic resonance imagesData augmentationClassification taskSpecific cognitive tasksMedical image analysisSynthetic data augmentationEffective data augmentationDownstream learning tasksCognitive tasksVariational autoencoder modelLearning taskTraining dataAutoencoder modelTemporal informationTraining datasetSequential informationSynthetic imagesTaskFMRI sequencesImage analysisMultiple perspectivesMagnetic resonance imagesImagesDifferent alternativesPersistent issue
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
2011
Unified 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 useFrameworkPlatform
2009
Unified framework for development, deployment and testing of image analysis algorithms
Joshi A, Scheinost D, Okuda H, Murphy I, Staib L, Papademetris X. Unified framework for development, deployment and testing of image analysis algorithms. The MIDAS Journal 2009 DOI: 10.54294/pq6gf6.Peer-Reviewed Original ResearchImage analysis algorithmsUser interface controlsUser interfaceAnalysis algorithmCommand-line user interfaceGraphical user interface controlsPlatform interoperabilityInterface controlSource codeComplex algorithmsSuch algorithmsNovel frameworkFramework idealMultiple platformsUnified frameworkAlgorithmRapid developmentDeploymentCustom pipelineImage analysisUsersPublic useFrameworkInteroperabilityDevelopers
2006
BioImage Suite: An integrated medical image analysis suite: An update.
Papademetris X, Jackowski MP, Rajeevan N, DiStasio M, Okuda H, Constable RT, Staib LH. BioImage Suite: An integrated medical image analysis suite: An update. Insight Journal 2006, 2006: 209. PMID: 25364771, PMCID: PMC4213804, DOI: 10.54294/2g80r4.Peer-Reviewed Original ResearchVisualization ToolkitInsight ToolkitUser-friendly user interfaceTcl scripting languageArea of segmentationAnalysis software suiteScripting languageUser interfaceImage processingBioImage SuiteSoftware suiteAdditional algorithmsAnalysis suiteBeta versionImage analysisToolkitSuiteSegmentationDownloadAlgorithmLanguageYaleRegistrationProcessingUpdate
1998
Volumetric layer segmentation using coupled surfaces propagation
Zeng X, Staib L, Schultz R, Duncan J. Volumetric layer segmentation using coupled surfaces propagation. 2015 IEEE Conference On Computer Vision And Pattern Recognition (CVPR) 1998, 708-715. DOI: 10.1109/cvpr.1998.698681.Peer-Reviewed Original ResearchMedical image analysisUseful image informationMagnetic resonance brain imagesImage-derived informationImage gradient informationLevel set implementationGray level valuesEasy initializationSegmentation problemImage informationAutomatic segmentationGradient informationSet implementationBrain imagesLayer segmentationComputational efficiencyNon-brain structuresLeft ventricle myocardiumImage analysisSegmentationInformationNew approachTest examplesSurface propagationVentricle myocardium
1996
Deformable boundary finding in medical images by integrating gradient and region information
Chakraborty A, Staib L, Duncan J. Deformable boundary finding in medical images by integrating gradient and region information. IEEE Transactions On Medical Imaging 1996, 15: 859-870. PMID: 18215965, DOI: 10.1109/42.544503.Peer-Reviewed Original ResearchBoundary findingMedical imagesHomogeneous region-classified areaBiomedical image analysisGray level homogeneityRegion-based segmentationReal medical imagesComputational overheadImage segmentationRegion informationShape informationPoor initializationPerceptual notionsImage analysisNumber of experimentsSegmentationVariety of limitationsGreen's theoremImagesUnified approachAuthors' approachKey issuesNew approachOverheadInformation
1994
Deformable boundary finding influenced by region homogeneity
Chakraborty A, Staib L, Duncan J. Deformable boundary finding influenced by region homogeneity. 2015 IEEE Conference On Computer Vision And Pattern Recognition (CVPR) 1994, 624-627. DOI: 10.1109/cvpr.1994.323790.Peer-Reviewed Original ResearchHomogeneous region-classified areaGray level homogeneityBoundary findingBiomedical image analysisRegion-based segmentationImage segmentationShape informationGreen's theoremPoor initializationConventional methodsPerceptual notionsRegion homogeneityImage analysisVariety of limitationsSegmentationUnified approachKey issuesAn integrated approach to boundary finding in medical images
Chakraborty A, Staib L, Duncan J. An integrated approach to boundary finding in medical images. 1994, 13-22. DOI: 10.1109/bia.1994.315870.Peer-Reviewed Original ResearchBoundary findingMedical imagesHomogeneous region-classified areaBiomedical image analysisGray level homogeneityReal medical imagesImage segmentationShape informationPoor initializationPerceptual notionsImage analysisNumber of experimentsSegmentationVariety of limitationsConventional gradientImagesUnified approachAuthors' approachKey issuesNew approachGreen's theoremConventional methodsIntegrated approachInitializationFinder
1990
Medical image analysis using model-based optimization
Duncan J, Staib L, Birkholzer T, Owen R, Anandan P, Bozma I. Medical image analysis using model-based optimization. 1990, 370-377. DOI: 10.1109/vbc.1990.109344.Peer-Reviewed Original ResearchMedical image analysisObject recognition problemOutlines of objectsModel-based optimizationRecognition problemExtracting featuresSegmented objectsOptimization theoryMathematical modelMedical imagingObject shapeUnifying approachAnalysis problemImage analysisThird exampleQuantitative descriptionObjectsMovement propertiesProblemSegmentationAnalysis methodPurpose of diagnosisOptimizationExampleMotion