2022
Manifold Learning via Linear Tangent Space Alignment (LTSA) for Accelerated Dynamic MRI With Sparse Sampling
Djebra Y, Marin T, Han P, Bloch I, Fakhri G, Ma C. Manifold Learning via Linear Tangent Space Alignment (LTSA) for Accelerated Dynamic MRI With Sparse Sampling. IEEE Transactions On Medical Imaging 2022, 42: 158-169. PMID: 36121938, PMCID: PMC10024645, DOI: 10.1109/tmi.2022.3207774.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputer SimulationImage Processing, Computer-AssistedMagnetic Resonance ImagingModels, TheoreticalConceptsSpace alignmentSampled k-space dataState-of-the-art methodsIntrinsic low-dimensional manifold structureNumerical simulation studyLow-dimensional manifold structureState-of-the-artLinear subspace modelSparsity modelModel-based frameworkSubspace modelManifold structureMathematical modelManifold modelSparse samplingImage reconstructionMRI applicationsDynamic magnetic resonance imagingSpatiotemporal signalsSpatial resolutionPerformanceSimulation studyImagesMethodSparsityJoint spectral quantification of MR spectroscopic imaging using linear tangent space alignment‐based manifold learning
Ma C, Han P, Zhuo Y, Djebra Y, Marin T, Fakhri G. Joint spectral quantification of MR spectroscopic imaging using linear tangent space alignment‐based manifold learning. Magnetic Resonance In Medicine 2022, 89: 1297-1313. PMID: 36404676, PMCID: PMC9892363, DOI: 10.1002/mrm.29526.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBrainComputer SimulationHumansMagnetic Resonance ImagingMagnetic Resonance SpectroscopyProton Magnetic Resonance SpectroscopyConceptsSubspace-based methodsManifold learningIntrinsic low-dimensional structureGlobal coordinationLearning-based methodsNumerical simulation dataSpatial smoothness constraintSparsity constraintSpace alignmentSubspace modelSmoothness constraintSuperior performanceRoot mean square errorLinear transformationMechanical simulationsLow-dimensionalSquare errorSubspaceExperimental dataSpectroscopic imagingQuantum mechanical simulationsCoordinate alignmentMR spectroscopic imagingSpectral quantificationSimulated dataPosterior estimation using deep learning: a simulation study of compartmental modeling in dynamic positron emission tomography
Liu X, Marin T, Amal T, Woo J, Fakhri G, Ouyang J. Posterior estimation using deep learning: a simulation study of compartmental modeling in dynamic positron emission tomography. Medical Physics 2022, 50: 1539-1548. PMID: 36331429, PMCID: PMC10087283, DOI: 10.1002/mp.16078.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremComputer SimulationDeep LearningNeural Networks, ComputerPositron-Emission TomographyConceptsConditional variational auto-encoderDeep learning approachNeural networkDeep learningMarkov chain Monte CarloVariational Bayesian inference frameworkLearning approachDeep learning-based approachVariational auto-encoderDeep neural networksLearning-based approachDynamic brain PET imagingPosterior distributionEstimate posterior distributionsBayesian inference frameworkAuto-encoderMedical imagesInference frameworkNetworkSimulation studyBrain PET imagingLearningPosterior estimatesInferior performanceImages
2020
PET imaging of neurotransmission using direct parametric reconstruction
Petibon Y, Alpert N, Ouyang J, Pizzagalli D, Cusin C, Fava M, Fakhri G, Normandin M. PET imaging of neurotransmission using direct parametric reconstruction. NeuroImage 2020, 221: 117154. PMID: 32679252, PMCID: PMC7800040, DOI: 10.1016/j.neuroimage.2020.117154.Peer-Reviewed Original ResearchMeSH KeywordsBrainComputer SimulationHumansNeuroimagingPositron-Emission TomographyRadiopharmaceuticalsSynaptic TransmissionConceptsSignal-to-noise ratioImage reconstructionPositron emission tomography image reconstructionLow signal-to-noise ratioPoisson log-likelihood functionScattered coincidencesDetector sensitivityPET sinogramsStatistical fluctuationsEstimate parametric imagesGradient-based optimizationParametric reconstructionLog-likelihood functionEffects of head movementVoxel scalePositron emission tomographySimplified reference region modelActivity concentration data
2018
Iterative PET Image Reconstruction Using Convolutional Neural Network Representation
Gong K, Guan J, Kim K, Zhang X, Yang J, Seo Y, Fakhri G, Qi J, Li Q. Iterative PET Image Reconstruction Using Convolutional Neural Network Representation. IEEE Transactions On Medical Imaging 2018, 38: 675-685. PMID: 30222554, PMCID: PMC6472985, DOI: 10.1109/tmi.2018.2869871.Peer-Reviewed Original ResearchMeSH KeywordsComputer SimulationHumansImage Processing, Computer-AssistedLikelihood FunctionsNeural Networks, ComputerPositron-Emission TomographyConceptsPET image reconstructionNeural networkConvolutional neural network representationsDeep residual convolutional neural networkImage reconstructionResidual convolutional neural networkComputer vision tasksDeep neural networksConvolutional neural networkNeural network denoisersAlternating direction methodNeural network representationIterative reconstruction frameworkNeural network methodVision tasksImage representationNetwork denoisingReconstruction frameworkMultipliers algorithmMedical imagesOptimization problemNetwork methodPost-processing toolDirection methodNetwork representation
2017
Use of Monte Carlo Techniques in Nuclear Medicine
Fahey F, Grogg K, Fakhri G. Use of Monte Carlo Techniques in Nuclear Medicine. Journal Of The American College Of Radiology 2017, 15: 446-448. PMID: 29173989, PMCID: PMC6335966, DOI: 10.1016/j.jacr.2017.09.045.Peer-Reviewed Original ResearchSimulation study of light transport in laser-processed LYSO:Ce detectors with single-side readout
Bläckberg L, Fakhri G, Sabet H. Simulation study of light transport in laser-processed LYSO:Ce detectors with single-side readout. Physics In Medicine And Biology 2017, 62: 8419-8440. PMID: 29047453, PMCID: PMC5736368, DOI: 10.1088/1361-6560/aa8dea.Peer-Reviewed Original ResearchMeSH KeywordsCerium RadioisotopesComputer SimulationEquipment DesignLasersLightPhotonsScintillation CountingConceptsDetector typesLYSO:Ce detectorsLYSO:Ce crystalsBarrier refractive indexScintillation light transportImproved energy resolutionRefractive indexLaser-processed crystalsCollection efficiencyLight transportPixel-like patternScintillation lightMPPC arraysEnergy resolutionPixel arrayDOI informationPulsed laser beamLight response functionLine profilesCe crystalsMonolithic crystalsBarrier patternsCrystal bulkTime resolutionCE detector
2016
Validation of Bayesian analysis of compartmental kinetic models in medical imaging
Sitek A, Li Q, Fakhri G, Alpert N. Validation of Bayesian analysis of compartmental kinetic models in medical imaging. Physica Medica 2016, 32: 1252-1258. PMID: 27692754, PMCID: PMC5720163, DOI: 10.1016/j.ejmp.2016.09.010.Peer-Reviewed Original ResearchConceptsAccurate estimation of uncertaintyComputer simulationsMedical imagesPosterior distributionDistributed noiseTime series of imagesClosed-formSeries of imagesData setsKinetic parametersMarkov chain Monte Carlo methodsPosterior distributions of kinetic parametersNon-linear least squares methodAccurate estimationComputerLeast-squares methodKinetic modelEstimation of kinetic parametersF18-fluorodeoxyglucoseBayesian estimationImagesStatistical inferenceMonte Carlo methodEstimates of uncertaintyInformationPharmacokinetic Evaluation of the Tau PET Radiotracer 18F-T807 (18F-AV-1451) in Human Subjects
Wooten D, Guehl N, Verwer E, Shoup T, Yokell D, Zubcevik N, Vasdev N, Zafonte R, Johnson K, Fakhri G, Normandin M. Pharmacokinetic Evaluation of the Tau PET Radiotracer 18F-T807 (18F-AV-1451) in Human Subjects. Journal Of Nuclear Medicine 2016, 58: 484-491. PMID: 27660144, PMCID: PMC5334185, DOI: 10.2967/jnumed.115.170910.Peer-Reviewed Original ResearchConceptsDistribution volume ratioTraumatic brain injuryMetabolite-corrected arterial input functionPET imagingPlasma radioactivity concentrationsTemporal cortexDynamic PET imagesTotal volume of distributionVolume of distributionTraumatic brain injury subjectsMesial temporal cortexArterial blood samplesPosterior cingulate gyrusFocal uptakeSUV ratioHuman subjectsArterial input functionPosterior corpus callosumBolus injectionPharmacokinetic evaluation
2015
Pulmonary imaging using respiratory motion compensated simultaneous PET/MR
Dutta J, Huang C, Li Q, El Fakhri G. Pulmonary imaging using respiratory motion compensated simultaneous PET/MR. Medical Physics 2015, 42: 4227-4240. PMID: 26133621, PMCID: PMC4474958, DOI: 10.1118/1.4921616.Peer-Reviewed Original ResearchConceptsRespiratory motionContrast-to-noise ratioClinical patient studiesPulse sequenceHigh-intensity featuresXCAT studyLow proton densityXCAT simulationPatient studiesXCAT phantomAttenuation mapBiograph mMRComplete data acquisitionSimultaneous PET/MRNonrigid registrationPET/MR scannersPET/magnetic resonanceMagnetic susceptibilityProton densityQuantitative accuracyRelaxation timePulmonary imagingLung lesionsBlurring artifactsDeformation field
2014
Sparse-View Spectral CT Reconstruction Using Spectral Patch-Based Low-Rank Penalty
Kim K, Ye J, Worstell W, Ouyang J, Rakvongthai Y, Fakhri G, Li Q. Sparse-View Spectral CT Reconstruction Using Spectral Patch-Based Low-Rank Penalty. IEEE Transactions On Medical Imaging 2014, 34: 748-760. PMID: 25532170, DOI: 10.1109/tmi.2014.2380993.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAtherosclerosisComputer SimulationHumansPhantoms, ImagingPoisson DistributionSpectrometry, X-Ray EmissionTomography, X-Ray ComputedConceptsLow-rank penaltySelf-similarity of patchesLog-likelihoodPoisson log-likelihoodCost functionSpectral CT reconstructionOriginal cost functionGPU implementationAlternating minimizationSensitive to intensity changesConventional algorithmsSpectral imagingEdge directionComputational costProcedure algorithmComputational advantagesAlgorithmX-ray transmissionComputer simulationsOptimization methodSpectral computed tomographySelf-similarityCT reconstructionX-rayGPU4D numerical observer for lesion detection in respiratory‐gated PET
Lorsakul A, Li Q, Trott C, Hoog C, Petibon Y, Ouyang J, Laine A, Fakhri G. 4D numerical observer for lesion detection in respiratory‐gated PET. Medical Physics 2014, 41: 102504. PMID: 25281979, PMCID: PMC4281099, DOI: 10.1118/1.4895975.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputer SimulationFluorodeoxyglucose F18HumansImage Interpretation, Computer-AssistedLung DiseasesModels, BiologicalMonte Carlo MethodMotionPhantoms, ImagingPositron-Emission TomographyRadiopharmaceuticalsRegression AnalysisRespiratory-Gated Imaging TechniquesSignal-To-Noise RatioConceptsRespiratory-gated positron emission tomographyMotion-corrected imagesDetection signal-to-noise ratioLesion detection taskNumerical observationsLesion detection performanceSignal-to-noise ratioPositron emission tomography sinogramsSpherical lesionsHotelling observerMotion correction methodPositron emission tomographyGeant4 ApplicationTomographic EmissionChannelized Hotelling observerAnthropomorphic phantomScanner geometryOSEM algorithmMonte Carlo simulationsPET framesImprove lesion detectionLesion detectionSignal-to-noise ratio measurementsActivity distributionConventional 3D approachSpectral CT Using Multiple Balanced K-Edge Filters
Rakvongthai Y, Worstell W, Fakhri G, Bian J, Lorsakul A, Ouyang J. Spectral CT Using Multiple Balanced K-Edge Filters. IEEE Transactions On Medical Imaging 2014, 34: 740-747. PMID: 25252276, PMCID: PMC4349342, DOI: 10.1109/tmi.2014.2358561.Peer-Reviewed Original ResearchConceptsK-edge filtersReconstructed attenuation coefficientsEnergy binsAttenuation coefficientMultiple energy binsX-ray sourcesX-ray tubeBack-projection reconstructionSpectral CT imagingTransmission matrixModel expectationsSinogram binsBeam hardeningComplex phantomsSpectral computed tomographyK-edgeAttenuation imagesSpectral CTCT scannerX-rayConventional detectorsBack-projectionSinogramPhantomCost-effective system designEffect of time‐of‐flight and point spread function modeling on detectability of myocardial defects in PET
Schaefferkoetter J, Ouyang J, Rakvongthai Y, Nappi C, El Fakhri G. Effect of time‐of‐flight and point spread function modeling on detectability of myocardial defects in PET. Medical Physics 2014, 41: 062502. PMID: 24877836, PMCID: PMC4032408, DOI: 10.1118/1.4875725.Peer-Reviewed Original ResearchConceptsSignal-to-noise ratioDetection signal-to-noise ratioPoint spread functionObserver signal-to-noise ratioEffects of time-of-flightMyocardial defectsHuman observer performanceDefect detectionSlow convergenceTime-of-flight (TOFNon-PSFPostreconstruction smoothingFDG-PET dataTime-of-flightPSF reconstructionCombination of TOFNon-TOFIterationObserver performanceClinical practiceSpread functionReconstruction parametersReconstruction protocolsIterative methodDetectionTowards coronary plaque imaging using simultaneous PET-MR: a simulation study
Petibon Y, Fakhri G, Nezafat R, Johnson N, Brady T, Ouyang J. Towards coronary plaque imaging using simultaneous PET-MR: a simulation study. Physics In Medicine And Biology 2014, 59: 1203-1222. PMID: 24556608, PMCID: PMC4061607, DOI: 10.1088/0031-9155/59/5/1203.Peer-Reviewed Original ResearchMeSH KeywordsComputer SimulationCoronary AngiographyCoronary StenosisHumansImage Interpretation, Computer-AssistedImaging, Three-DimensionalMagnetic Resonance AngiographyModels, CardiovascularMultimodal ImagingPhantoms, ImagingPositron-Emission TomographyReproducibility of ResultsSensitivity and SpecificityConceptsSimultaneous PET-MRChannelized Hotelling observerAttenuation mapMotion correctionPET-MRFluorodeoxyglucose-positron emission tomography imagingRespiratory motion fieldsMotion correction methodCho SNRMotion correction techniqueAnthropomorphic phantomUncorrected reconstructionsRespiratory motionXCAT phantomCoronary plaque imagingMonte Carlo simulationsPET reconstructionXCATActivity distributionCardiac gatingNon-rigid registrationHotelling observerCarlo simulationsPlaque imagingPhantom
2013
Dual-Tracer PET Using Generalized Factor Analysis of Dynamic Sequences
El Fakhri G, Trott C, Sitek A, Bonab A, Alpert N. Dual-Tracer PET Using Generalized Factor Analysis of Dynamic Sequences. Molecular Imaging And Biology 2013, 15: 666-674. PMID: 23636489, PMCID: PMC3812387, DOI: 10.1007/s11307-013-0631-1.Peer-Reviewed Original ResearchConceptsEmit gamma raysPositron emission tomographyNear-simultaneous imagingSingle-photon emissionBrain PET studiesGamma raysSingle-photon emission computed tomographyActivity distributionRaclopride studiesEmission computed tomographyPositron emission tomography radiopharmaceuticalsSimultaneous imagingD2 bindingFactor analysis of dynamic sequencesActivity estimationTime activity curvesRacloprideFDGRhesus monkeysEmission tomographyPET studiesActivation curveBrain metabolismEmissionSimulate human data
2009
Monte Carlo modeling of cascade gamma rays in 86Y PET imaging: preliminary results
Zhu X, Fakhri G. Monte Carlo modeling of cascade gamma rays in 86Y PET imaging: preliminary results. Physics In Medicine And Biology 2009, 54: 4181-4193. PMID: 19521011, PMCID: PMC3111055, DOI: 10.1088/0031-9155/54/13/014.Peer-Reviewed Original ResearchConceptsCascade gamma raysScatter fractionGamma raysPhoton energy distributionLow count ratesHigh-energy photonsMonte Carlo programScatter correction methodGATE simulation packageMonte Carlo modelDevelopment of correction methodsSpatial resolutionGamma photonsEnergy windowCount rateScattering eventsRandom coincidencesEnergy distributionPhantom acquisitionsPersonal dosimetryPET imagingVariance reduction techniquesPhotonsCorrection methodSimSET
2005
Collimator Optimization for Detection and Quantitation Tasks: Application to Gallium-67 Imaging
Moore S, Kijewski M, Fakhri G. Collimator Optimization for Detection and Quantitation Tasks: Application to Gallium-67 Imaging. IEEE Transactions On Medical Imaging 2005, 24: 1347-1356. PMID: 16229420, DOI: 10.1109/tmi.2005.857211.Peer-Reviewed Original ResearchMeSH KeywordsCitratesComputer SimulationComputer-Aided DesignEquipment DesignEquipment Failure AnalysisGalliumHumansImage EnhancementImage Interpretation, Computer-AssistedModels, BiologicalNeoplasmsPhantoms, ImagingPositron-Emission TomographyRadiopharmaceuticalsReproducibility of ResultsSensitivity and SpecificityConceptsMedium-energy low-penetration collimatorCollimator optimizationGeometric spatial resolutionPhotopeak energy windowSimulation of photon transportLead X-raysClinical imaging tasksActivity estimation taskSignal-to-noise ratioGallium-67 imagingContaminating photonsEnergy windowGeometric efficiencyCollimator designFixed energyPhoton transportOptimal collimatorCollimatorHotelling observerFWHMSpatial resolutionNuclear medicineDetectorResolution valuesImaging tasksQuantitative dynamic cardiac 82Rb PET using generalized factor and compartment analyses.
El Fakhri G, Sitek A, Guérin B, Kijewski M, Di Carli M, Moore S. Quantitative dynamic cardiac 82Rb PET using generalized factor and compartment analyses. Journal Of Nuclear Medicine 2005, 46: 1264-71. PMID: 16085581.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAlgorithmsComputer SimulationCoronary Artery DiseaseFeasibility StudiesFemaleHeartHumansImage Interpretation, Computer-AssistedMaleMiddle AgedModels, CardiovascularPositron-Emission TomographyRadiopharmaceuticalsReproducibility of ResultsRubidium RadioisotopesSensitivity and SpecificitySeverity of Illness IndexConceptsMyocardial perfusionAbsolute myocardial perfusionCatheterization resultsMyocardial tissue extractsDipyridamole stressCardiac PETClinical valueMyocardial factorsFactor analysis of dynamic sequencesPatient studiesLVNoninvasive estimationAccurate input functionPatientsCompartment analysisAverage errorPerfusionParametric mappingTissue extractsRV contributionRV
2002
Optimization of Ga‐67 imaging for detection and estimation tasks: Dependence of imaging performance on spectral acquisition parameters
Fakhri G, Moore S, Kijewski M. Optimization of Ga‐67 imaging for detection and estimation tasks: Dependence of imaging performance on spectral acquisition parameters. Medical Physics 2002, 29: 1859-1866. PMID: 12201433, DOI: 10.1118/1.1493214.Peer-Reviewed Original ResearchConceptsIdeal signal-to-noise ratioEnergy windowSignal-to-noise ratioMonte Carlo programDetection of spheresTorso phantomPhantom acquisitionsSphere of radiusEstimation taskPhantom dataLower-energyGa-67 imagingPhantomAcquisition parametersActivity concentrationsSpectral acquisition parametersGa-67Sphere sizeEnergyPhotopeakTumor imagingOptimal windowTaskClinicMonte