2022
(Un)common space in infant neuroimaging studies: A systematic review of infant templates
Dufford AJ, Hahn CA, Peterson H, Gini S, Mehta S, Alfano A, Scheinost D. (Un)common space in infant neuroimaging studies: A systematic review of infant templates. Human Brain Mapping 2022, 43: 3007-3016. PMID: 35261126, PMCID: PMC9120551, DOI: 10.1002/hbm.25816.Peer-Reviewed Original ResearchBrainDiffusion Magnetic Resonance ImagingHumansImage Processing, Computer-AssistedInfantInfant, NewbornMagnetic Resonance ImagingNeuroimaging
2019
A decade of test-retest reliability of functional connectivity: A systematic review and meta-analysis
Noble S, Scheinost D, Constable RT. A decade of test-retest reliability of functional connectivity: A systematic review and meta-analysis. NeuroImage 2019, 203: 116157. PMID: 31494250, PMCID: PMC6907736, DOI: 10.1016/j.neuroimage.2019.116157.Peer-Reviewed Original ResearchMeSH KeywordsBrainBrain MappingHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingNeural PathwaysReproducibility of ResultsConceptsIntraclass correlation coefficientTest-retest reliabilityFunctional connectivitySystematic reviewShort test-retest intervalsTest-retest reliability studyIndividual edgesNarrative summaryTest-retest intervalSearch of ScopusMeta-analytic estimatesCortical edgeRandom effectsQualitative reviewNeuroscience toolsReviewActive recordingReview of factorsExpense of validitySubject dataStudyDynamic‐flip‐angle ECG‐gating with nuisance signal regression improves resting‐state BOLD functional connectivity mapping by reducing cardiogenic noise
Hu C, Tokoglu F, Scheinost D, Qiu M, Shen X, Peters DC, Galiana G, Constable RT. Dynamic‐flip‐angle ECG‐gating with nuisance signal regression improves resting‐state BOLD functional connectivity mapping by reducing cardiogenic noise. Magnetic Resonance In Medicine 2019, 82: 911-923. PMID: 31016782, DOI: 10.1002/mrm.27775.Peer-Reviewed Original Research
2017
An exemplar-based approach to individualized parcellation reveals the need for sex specific functional networks
Salehi M, Karbasi A, Shen X, Scheinost D, Constable RT. An exemplar-based approach to individualized parcellation reveals the need for sex specific functional networks. NeuroImage 2017, 170: 54-67. PMID: 28882628, PMCID: PMC5905726, DOI: 10.1016/j.neuroimage.2017.08.068.Peer-Reviewed Original ResearchMeSH KeywordsAdultBrainBrain MappingFemaleHumansImage Processing, Computer-AssistedMaleModels, TheoreticalNerve NetSex CharacteristicsConceptsIndividualized parcellationParcellation techniqueFunctional networksCross-validated predictive modelSpecific functional networksCerebral cortexPatient subgroupsFunctional connectivity dataFunctional organizationBrainParcellation schemesClinical applicationParcellation approachParcellationSexSubgroupsConnectivity dataIndividualized studyNetwork organizationIndividualsAmple evidencePatientsCortexMulti-modal analysis of functional connectivity and cerebral blood flow reveals shared and unique effects of propofol in large-scale brain networks
Qiu M, Scheinost D, Ramani R, Constable RT. Multi-modal analysis of functional connectivity and cerebral blood flow reveals shared and unique effects of propofol in large-scale brain networks. NeuroImage 2017, 148: 130-140. PMID: 28069540, PMCID: PMC5410383, DOI: 10.1016/j.neuroimage.2016.12.080.Peer-Reviewed Original ResearchConceptsCerebral blood flowIntrinsic connectivity distributionLarge-scale brain networksFunctional connectivityReduced consciousnessBlood flowBrain networksSedation conditionsWhole-brain connectivityAltered connectivityMotor networkCBF dataRs-fMRIPharmacological alterationsConnectivity differencesPropofolMultiple large-scale brain networksUnique neural correlatesBlow flowFrontoparietal networkAnesthesiaKey markersDefault modeNeural correlatesSame subjects
2016
Fluctuations in Global Brain Activity Are Associated With Changes in Whole-Brain Connectivity of Functional Networks
Scheinost D, Tokoglu F, Shen X, Finn ES, Noble S, Papademetris X, Constable RT. Fluctuations in Global Brain Activity Are Associated With Changes in Whole-Brain Connectivity of Functional Networks. IEEE Transactions On Biomedical Engineering 2016, 63: 2540-2549. PMID: 27541328, PMCID: PMC5180443, DOI: 10.1109/tbme.2016.2600248.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAgedAlgorithmsBrainFemaleHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMaleMiddle AgedModels, StatisticalNerve NetRestSignal Processing, Computer-AssistedYoung AdultConceptsGlobal brain activityResting-state networksWhole-brain connectivityBrain activityResting-state functional magnetic resonance imagingTime pointsFunctional resting-state networksFunctional magnetic resonance imagingMagnetic resonance imagingResting-state studyBrain statesRSN connectivitySensory functionSubcortical regionsResonance imagingCognitive functionCoactivation patternsUnique brain statesBrain connectivityActivity stateCritical time pointsFunctional networksSignal intensityVoxel-based methodBrain dynamics
2015
Alterations in Anatomical Covariance in the Prematurely Born
Scheinost D, Kwon SH, Lacadie C, Vohr BR, Schneider KC, Papademetris X, Constable RT, Ment LR. Alterations in Anatomical Covariance in the Prematurely Born. Cerebral Cortex 2015, 27: 534-543. PMID: 26494796, PMCID: PMC5939217, DOI: 10.1093/cercor/bhv248.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentBrainFemaleHumansImage Processing, Computer-AssistedInfant, PrematureMagnetic Resonance ImagingMaleNeural PathwaysOrgan SizeProspective StudiesYoung AdultPreterm birth alters neonatal, functional rich club organization
Scheinost D, Kwon SH, Shen X, Lacadie C, Schneider KC, Dai F, Ment LR, Constable RT. Preterm birth alters neonatal, functional rich club organization. Brain Structure And Function 2015, 221: 3211-3222. PMID: 26341628, PMCID: PMC4779074, DOI: 10.1007/s00429-015-1096-6.Peer-Reviewed Original ResearchMeSH KeywordsBrainBrain MappingFemaleHumansImage Processing, Computer-AssistedInfant, NewbornInfant, PrematureMagnetic Resonance ImagingMaleNeural PathwaysConceptsPT neonatesTerm neonatesRich-club organizationPreterm birth altersTerm-equivalent ageClub organizationFunctional magnetic resonance imagingMagnetic resonance imagingPT birthBirth altersWhole-brain networksNeonatesResonance imagingPretermFunctional connectivityFunctional segregationCognitive difficultiesEquivalent ageFunctional organizationBrainThe (in)stability of functional brain network measures across thresholds
Garrison KA, Scheinost D, Finn ES, Shen X, Constable RT. The (in)stability of functional brain network measures across thresholds. NeuroImage 2015, 118: 651-661. PMID: 26021218, PMCID: PMC4554838, DOI: 10.1016/j.neuroimage.2015.05.046.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedBrainBrain MappingFemaleHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMaleMiddle AgedModels, NeurologicalNerve NetNeuroimagingYoung AdultConceptsBinary graph
2014
Optimizing real time fMRI neurofeedback for therapeutic discovery and development
Stoeckel LE, Garrison KA, Ghosh S, Wighton P, Hanlon CA, Gilman JM, Greer S, Turk-Browne NB, deBettencourt MT, Scheinost D, Craddock C, Thompson T, Calderon V, Bauer CC, George M, Breiter HC, Whitfield-Gabrieli S, Gabrieli JD, LaConte SM, Hirshberg L, Brewer JA, Hampson M, Van Der Kouwe A, Mackey S, Evins AE. Optimizing real time fMRI neurofeedback for therapeutic discovery and development. NeuroImage Clinical 2014, 5: 245-255. PMID: 25161891, PMCID: PMC4141981, DOI: 10.1016/j.nicl.2014.07.002.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsBrain MappingHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingNeurofeedbackConceptsBrain disordersBrain functionReal-time functional magnetic resonance imaging (rt-fMRI) neurofeedbackRtfMRI neurofeedbackFunctional magnetic resonance imaging (fMRI) neurofeedbackWorld Health OrganizationEffective treatmentClinical problemBrain-behavior relationshipsTherapeutic toolEffective interventionsHealth OrganizationDisordersNational InstituteIntervention approachesTherapeutic discoveryNeurofeedbackPersonalized assessmentRtfMRIMaladaptive patternsMorbidityNeurotherapeuticsCoupled Intrinsic Connectivity Distribution Analysis: A Method for Exploratory Connectivity Analysis of Paired fMRI Data
Scheinost D, Shen X, Finn E, Sinha R, Constable RT, Papademetris X. Coupled Intrinsic Connectivity Distribution Analysis: A Method for Exploratory Connectivity Analysis of Paired fMRI Data. PLOS ONE 2014, 9: e93544. PMID: 24676034, PMCID: PMC3968179, DOI: 10.1371/journal.pone.0093544.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnesthesiaBrainBrain MappingCase-Control StudiesCocaine-Related DisordersHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingNeural PathwaysRestWakefulnessConceptsHealthy controlsIntrinsic connectivity distributionCocaine-dependent subjectsResting-state scansSeed-based analysisConnectivity analysisSimilar brain regionsBasic neuroscience researchMagnetic resonance imaging dataPsychiatric diseasesVoxel-based resultsConnectivity differencesBrain regionsClinical toolFunctional changesFunctional magnetic resonance imaging (fMRI) dataScansVoxel-based methodConnectivity approachNeuroscience researchConnectivity dataThe impact of image smoothness on intrinsic functional connectivity and head motion confounds
Scheinost D, Papademetris X, Constable RT. The impact of image smoothness on intrinsic functional connectivity and head motion confounds. NeuroImage 2014, 95: 13-21. PMID: 24657356, PMCID: PMC4076413, DOI: 10.1016/j.neuroimage.2014.03.035.Peer-Reviewed Original ResearchMeSH KeywordsArtifactsBrainBrain MappingFemaleHead MovementsHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMaleNeural PathwaysYoung AdultConceptsResting-state functional magnetic resonance imagingWhole-brain functional organizationFunctional magnetic resonance imagingIntrinsic functional connectivityMagnetic resonance imagingFunctional connectivity studiesResonance imagingRs-fMRIFunctional connectivityClinical populationsGroup differencesConnectivity studiesHead motionFunctional organizationHead movementsRecent studiesBOLD signal and functional connectivity associated with loving kindness meditation
Garrison KA, Scheinost D, Constable RT, Brewer JA. BOLD signal and functional connectivity associated with loving kindness meditation. Brain And Behavior 2014, 4: 337-347. PMID: 24944863, PMCID: PMC4055184, DOI: 10.1002/brb3.219.Peer-Reviewed Original ResearchMeSH KeywordsAdultBrainBrain MappingEmotionsFemaleHumansImage Processing, Computer-AssistedLoveMagnetic Resonance ImagingMaleMeditationMiddle AgedNerve NetConceptsPCC/PCuFunctional connectivityGreater functional connectivityIntrinsic connectivityPosterior cingulate cortex/precuneusParahippocampus/hippocampusSeed-based connectivity analysisBOLD signalBlood oxygen level-dependent (BOLD) signalGroup differencesIntrinsic connectivity distributionLevel-dependent signalKindness meditationCortical midline regionsDefault mode networkFunctional magnetic resonanceInsula lobeInferior frontal gyrusSilent repetitionBrain regionsLeft inferior frontal gyrusFrontal gyrusMidline regionSelf-related processingMode network
2013
Real-time fMRI links subjective experience with brain activity during focused attention
Garrison KA, Scheinost D, Worhunsky PD, Elwafi HM, Thornhill TA, Thompson E, Saron C, Desbordes G, Kober H, Hampson M, Gray JR, Constable RT, Papademetris X, Brewer JA. Real-time fMRI links subjective experience with brain activity during focused attention. NeuroImage 2013, 81: 110-118. PMID: 23684866, PMCID: PMC3729617, DOI: 10.1016/j.neuroimage.2013.05.030.Peer-Reviewed Original ResearchMeSH KeywordsAdultAttentionBrain MappingFemaleGyrus CinguliHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMaleMeditationMiddle AgedNeurofeedbackConceptsReal-time fMRIPosterior cingulate cortexBrain activitySubjective experienceFocused attentionCingulate cortexCognitive neuroscience researchFocused attention taskOngoing subjective experienceFeedback graphsOwn brain activityDefault mode networkAttention taskNeural processesIntrospective awarenessOngoing taskRt-fMRIAffective functionsExperienced meditatorsMode networkNovel contextNeuroscience researchMeditatorsBrain imagingObjective measuresA Graphics Processing Unit Accelerated Motion Correction Algorithm and Modular System for Real-time fMRI
Scheinost D, Hampson M, Qiu M, Bhawnani J, Constable RT, Papademetris X. A Graphics Processing Unit Accelerated Motion Correction Algorithm and Modular System for Real-time fMRI. Neuroinformatics 2013, 11: 291-300. PMID: 23319241, PMCID: PMC3644525, DOI: 10.1007/s12021-013-9176-3.Peer-Reviewed Case Reports and Technical NotesMeSH KeywordsAlgorithmsBrainBrain MappingComputer GraphicsHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMotionOxygenConceptsGraphics processing unitsNovel graphics processing unitMotion correction algorithmProcessing unitReal-time methodProcessing delayCorrection algorithmSystem designMotion correction strategiesOffline methodsAlgorithmAvailable softwareReal-time functional magnetic resonance imagingModular approachValuable featuresModular systemPresent algorithmReal-time fMRIMotion correctionMotion parametersSoftwareNew technologiesNew systemCorrection strategyEstimates of motion
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 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 useFrameworkPlatform
2010
New open‐source ictal SPECT analysis method implemented in BioImage Suite
Scheinost D, Teisseyre TZ, Distasio M, DeSalvo MN, Papademetris X, Blumenfeld H. New open‐source ictal SPECT analysis method implemented in BioImage Suite. Epilepsia 2010, 51: 703-707. PMID: 20074234, PMCID: PMC2963625, DOI: 10.1111/j.1528-1167.2009.02425.x.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBrainDominance, CerebralElectroencephalographyEpilepsies, PartialHumansImage Processing, Computer-AssistedSignal Processing, Computer-AssistedSubtraction TechniqueTomography, Emission-Computed, Single-Photon