2024
In vivo neuropil density from anatomical MRI and machine learning
Akif A, Staib L, Herman P, Rothman D, Yu Y, Hyder F. In vivo neuropil density from anatomical MRI and machine learning. Cerebral Cortex 2024, 34: bhae200. PMID: 38771239, PMCID: PMC11107380, DOI: 10.1093/cercor/bhae200.Peer-Reviewed Original ResearchMeSH KeywordsAdultBrainFemaleGray MatterHumansImage Processing, Computer-AssistedMachine LearningMagnetic Resonance ImagingMaleMiddle AgedNeural Networks, ComputerNeuropilPositron-Emission TomographyWhite MatterYoung AdultConceptsMagnetic resonance imagingSynaptic densityNeuropil densityCellular densityArtificial neural networkNeural networkPositron emission tomographyAnatomical magnetic resonance imagingHealthy subjectsSynaptic activityMRI scansMachine learning algorithmsBrain's energy budgetEmission tomographyIn vivo MRI scansResonance imagingTissue cellularityLearning algorithmsDiffusion magnetic resonance imagingMachine learningMicroscopic interpretationInterpretation of functional neuroimaging dataIndividual predictionsSubjects
2022
SimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation
You C, Zhou Y, Zhao R, Staib L, Duncan JS. SimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation. IEEE Transactions On Medical Imaging 2022, 41: 2228-2237. PMID: 35320095, PMCID: PMC10325835, DOI: 10.1109/tmi.2022.3161829.Peer-Reviewed Original ResearchMeSH KeywordsDistillationImage Processing, Computer-AssistedSupervised Machine LearningTomography, X-Ray ComputedConceptsMedical image segmentationImage segmentationSemi-supervised medical image segmentationRobust Medical Image SegmentationMedical image analysisUnsupervised training strategyAtrial Segmentation ChallengeLearning-based approachMedical image synthesisAverage Dice scoreSemi-supervised approachPair-wise similarityContrastive objectiveData augmentationSegmentation challengePopular datasetsDice scoreSemantic informationDistillation frameworkSegmentation accuracyDownstream tasksImage synthesisPrevious best resultSupervised counterpartMedical data
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 ResearchMeSH KeywordsAlgorithmsAnimalsBrainDeep LearningDogsEchocardiographyHeart VentriclesHumansImage Processing, Computer-AssistedImaging, Three-DimensionalMachine LearningModels, TheoreticalNeural Networks, ComputerTomography, X-Ray Computed
2018
Segmenting 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 Computed
2016
Pivotal 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 ResearchMeSH KeywordsAutism Spectrum DisorderBayes TheoremBehavior TherapyBrainChildChild, PreschoolFemaleHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMaleNeural PathwaysOxygenConceptsPivotal Response TreatmentAutism spectrum disorderOccipital-temporal cortexAttentional systemResponse treatmentSpectrum disorderOrbitofrontal cortexPosterior cingulateHigh-level objectsBehavioral interventionsLearning mechanismPerception shiftProcessing areasNeural circuitsFunctional rewiringCortexTreatment regimenAutismInterventionNovel Bayesian frameworkCingulateFunctional changesIndividualsDisordersObjects
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
2014
Using SUV as a Guide to 18F-FDG Dose Reduction
Cheng DW, Ersahin D, Staib LH, Della Latta D, Giorgetti A, d’Errico F. Using SUV as a Guide to 18F-FDG Dose Reduction. Journal Of Nuclear Medicine 2014, 55: 1998-2002. PMID: 25453048, DOI: 10.2967/jnumed.114.140129.Peer-Reviewed Original ResearchDiffusion Tensor Imaging as a Predictor of Locomotor Function after Experimental Spinal Cord Injury and Recovery
Kelley BJ, Harel NY, Kim CY, Papademetris X, Coman D, Wang X, Hasan O, Kaufman A, Globinsky R, Staib LH, Cafferty WB, Hyder F, Strittmatter SM. Diffusion Tensor Imaging as a Predictor of Locomotor Function after Experimental Spinal Cord Injury and Recovery. Journal Of Neurotrauma 2014, 31: 1362-1373. PMID: 24779685, PMCID: PMC4120934, DOI: 10.1089/neu.2013.3238.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDiffusion Tensor ImagingDisease Models, AnimalFemaleImage Processing, Computer-AssistedImmunohistochemistryMotor ActivityPrognosisRatsRats, Sprague-DawleyRecovery of FunctionSpinal Cord InjuriesConceptsSpinal cord injuryDiffusion tensor imagingCord injuryAxonal integrityLocomotor functionExperimental spinal cord injuryTraumatic spinal cord injuryFemale Sprague-Dawley ratsTensor imagingFractional anisotropyFunctional recovery assessmentSpinal cord contusionLimited functional recoveryLong-term disabilityQuantitative diffusion tensor imagingRodent SCI modelsSprague-Dawley ratsSpinal cord morphologyWhite matter pathologyCaudal spinal cordWhite matter integrityInjury epicenterMidthoracic laminectomyCord contusionPrimary outcomeRadial 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 ResearchAlgorithmsAnimalsDogsEchocardiography, Four-DimensionalImage Processing, Computer-AssistedMaleMovementMyocardial InfarctionMyocardium
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 algorithm
2011
Targeted Imaging of the Spatial and Temporal Variation of Matrix Metalloproteinase Activity in a Porcine Model of Postinfarct Remodeling
Sahul ZH, Mukherjee R, Song J, McAteer J, Stroud RE, Dione DP, Staib L, Papademetris X, Dobrucki LW, Duncan JS, Spinale FG, Sinusas AJ. Targeted Imaging of the Spatial and Temporal Variation of Matrix Metalloproteinase Activity in a Porcine Model of Postinfarct Remodeling. Circulation Cardiovascular Imaging 2011, 4: 381-391. PMID: 21505092, PMCID: PMC3140564, DOI: 10.1161/circimaging.110.961854.Peer-Reviewed Original ResearchUnified 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 ResearchMeSH KeywordsAlgorithmsComputational BiologyDiagnostic ImagingHumansImage Processing, Computer-AssistedUser-Computer InterfaceConceptsUser 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 ResearchMeSH KeywordsAlgorithmsAnimalsFeasibility StudiesFemaleHumansImage Processing, Computer-AssistedImaging, Three-DimensionalPhantoms, ImagingTime FactorsTomographyUltrasonography, MammaryImage-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 acquisitionErrorEstimation
2005
ROC-based assessments of 3D cortical surface-matching algorithms
Bansal R, Staib LH, Whiteman R, Wang YM, Peterson BS. ROC-based assessments of 3D cortical surface-matching algorithms. NeuroImage 2005, 24: 150-162. PMID: 15588606, DOI: 10.1016/j.neuroimage.2004.08.054.Peer-Reviewed Original Research
2004
Geometric 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 ResearchMeSH KeywordsAlgorithmsBrainBrain MappingCerebral CortexComputer SimulationDiffusion Magnetic Resonance ImagingHumansImage Processing, Computer-AssistedModels, StatisticalNerve FibersNeural PathwaysConceptsApplied 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
Image Processing and Analysis at IPAG
Duncan JS, Staib LH. Image Processing and Analysis at IPAG. IEEE Transactions On Medical Imaging 2003, 22: 1505. PMID: 14649742, DOI: 10.1109/tmi.2003.819935.Peer-Reviewed Original ResearchMeSH KeywordsAcademic Medical CentersAlgorithmsForecastingHistory, 20th CenturyHistory, 21st CenturyImage EnhancementImage Processing, Computer-AssistedImaging, Three-DimensionalConceptsImage processing
2001
Automated measurement of latent morphological features in the human corpus callosum
Peterson B, Feineigle P, Staib L, Gore J. Automated measurement of latent morphological features in the human corpus callosum. Human Brain Mapping 2001, 12: 232-245. PMID: 11241874, PMCID: PMC6871880, DOI: 10.1002/1097-0193(200104)12:4<232::aid-hbm1018>3.0.co;2-j.Peer-Reviewed Original ResearchConceptsCorpus callosumSubject characteristicsYears of ageHuman corpus callosumPatient groupCallosum sizeHealthy subjectsMRI scansVentricular volumeCallosumMidsagittal planeFactor scoresNeural correlatesConstruct validityFactor-based analysisConventional measuresFuture studiesMorphological featuresAgePredictive validitySubjectsScoresNormal developmentVarimax rotationFactors