2024
Accelerated 3D metabolite T1 mapping of the brain using variable‐flip‐angle SPICE
Zhao Y, Li Y, Guo R, Jin W, Sutton B, Ma C, Fakhri G, Li Y, Luo J, Liang Z. Accelerated 3D metabolite T1 mapping of the brain using variable‐flip‐angle SPICE. Magnetic Resonance In Medicine 2024, 92: 1310-1322. PMID: 38923032, DOI: 10.1002/mrm.30200.Peer-Reviewed Original ResearchConceptsLow-rank tensor modelGeneralized series modelMetabolite TExperimental resultsBrain metabolitesClinically acceptable scan timeEfficient encodingPhantom experimental resultsAcceptable scan timeNoisy dataSparse samplingImaging problemsData processingHealthy subject dataVariable flip angleFlip angleTensor modelSaturation effectsQuantitative metabolic imagingMRSI techniquePhantomScan timeData acquisitionMetabolic imagingT1 mapping
2023
B1 inhomogeneity‐corrected T1 mapping and quantitative magnetization transfer imaging via simultaneously estimating Bloch‐Siegert shift and magnetization transfer effects
Jang A, Han P, Ma C, Fakhri G, Wang N, Samsonov A, Liu F. B1 inhomogeneity‐corrected T1 mapping and quantitative magnetization transfer imaging via simultaneously estimating Bloch‐Siegert shift and magnetization transfer effects. Magnetic Resonance In Medicine 2023, 90: 1859-1873. PMID: 37427533, PMCID: PMC10528411, DOI: 10.1002/mrm.29778.Peer-Reviewed Original ResearchConceptsBloch-Siegert shiftBloch-SiegertMagnetization transfer effectsMonte Carlo simulationsSpin-lattice relaxationSpin-bath modelMagnetization transferBinary spin-bath modelCarlo simulationsProton fractionOff-resonance irradiationIn vivo brain studiesBloch simulationsPhantom experimentsMagnetizationEstimationTransmitted fieldQuantitative magnetization transferMethod performanceMT effectSignal equationLongitudinal Imaging in a Patient With Opioid-associated Amnestic Syndrome
Barash J, Schmahmann J, Xie Z, Lev M, Fakhri G. Longitudinal Imaging in a Patient With Opioid-associated Amnestic Syndrome. Cognitive And Behavioral Neurology 2023, 36: 194-197. PMID: 37389894, PMCID: PMC10527331, DOI: 10.1097/wnn.0000000000000347.Peer-Reviewed Original ResearchMeSH KeywordsAdultAnalgesics, OpioidBrainCreatineFemaleHumansMagnetic Resonance ImagingOpioid-Related DisordersYoung AdultConceptsOpioid-associated amnestic syndromeFluid-attenuated inversion recoveryPositron emission tomographyAmnestic syndromeHistory of attention-deficit hyperactivity disorderAttention-deficit hyperactivity disorderBrain regions of individualsSubstance use disordersOpioid misuseMild memory lossN-acetyl aspartate/creatineUrine toxicology screenFollow-up imagingHistory of opioid misuseRegions of individualsTau depositionTau positron emission tomographyHyperactivity disorderIntravenous heroinRight hippocampusAnterograde amnesiaRestricted diffusionBrain regionsHippocampal abnormalitiesLongitudinal imagingArterial spin labeled perfusion imaging with balanced steady-state free precession readout and radial sampling
Han P, Marin T, Zhuo Y, Ouyang J, El Fakhri G, Ma C. Arterial spin labeled perfusion imaging with balanced steady-state free precession readout and radial sampling. Magnetic Resonance Imaging 2023, 102: 126-132. PMID: 37187264, PMCID: PMC10524790, DOI: 10.1016/j.mri.2023.05.005.Peer-Reviewed Original ResearchMeSH KeywordsArteriesBrainImage Processing, Computer-AssistedImaging, Three-DimensionalMagnetic Resonance ImagingPerfusionPerfusion ImagingSpin LabelsConceptsOff-resonance effectsBalanced steady-state free precessionPhase-cycling techniqueTemporal SNRBalanced steady-state free precession acquisitionRadial sampling schemeSpoiled gradient-recalled acquisitionRadial samplingCartesian sampling schemeBalanced steady-state free precession readoutK-space dataSampling schemeSpin labelingSteady-state free precessionK-spaceImage readoutBanding artifactsMotion-related artifactsReadoutFree precessionArterial spin labelingImage reconstructionParallel imagingImaging timePerfusion-weighted imaging
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 dataBrain MR Atlas Construction Using Symmetric Deep Neural Inpainting
Xing F, Liu X, Kuo C, Fakhri G, Woo J. Brain MR Atlas Construction Using Symmetric Deep Neural Inpainting. IEEE Journal Of Biomedical And Health Informatics 2022, 26: 3185-3196. PMID: 35139030, PMCID: PMC9250592, DOI: 10.1109/jbhi.2022.3149754.Peer-Reviewed Original ResearchConceptsImage inpainting methodInpainting methodDeep learning-based image inpainting methodsBrain Tumor Segmentation ChallengeMultimodal Brain Tumor Segmentation ChallengeReduce reconstruction errorAtlas constructionStatistical brain atlasInpainted regionsInpainted dataImage registration methodReconstruction errorTumor regionMutual informationSimilarity scoresSegmentation ChallengeSymmetry constraintsImage dataRegistration methodMagnetic resonance imagingTumor locationStatistical atlasDistribution of lesionsCross-correlationPatient populationVoxelHop: Successive Subspace Learning for ALS Disease Classification Using Structural MRI
Liu X, Xing F, Yang C, Kuo C, Babu S, Fakhri G, Jenkins T, Woo J. VoxelHop: Successive Subspace Learning for ALS Disease Classification Using Structural MRI. IEEE Journal Of Biomedical And Health Informatics 2022, 26: 1128-1139. PMID: 34339378, PMCID: PMC8807766, DOI: 10.1109/jbhi.2021.3097735.Peer-Reviewed Original ResearchConceptsConvolutional neural networkLearning modelsDimension reductionSubspace learning modelConcatenation of featuresState-of-the-artUnsupervised dimension reductionDeep learning modelsMedical image dataSupervised dimension reductionImage dataClassification of amyotrophic lateral sclerosisSubspace learningClassification taskDeep learningDataset sizeNeural networkSubspace approximationMemory requirementsTraining datasetClassification approachAUC scoreAccurate classificationDatasetExperimental results
2021
Free‐breathing 3D cardiac T1 mapping with transmit B1 correction at 3T
Han P, Marin T, Djebra Y, Landes V, Zhuo Y, Fakhri G, Ma C. Free‐breathing 3D cardiac T1 mapping with transmit B1 correction at 3T. Magnetic Resonance In Medicine 2021, 87: 1832-1845. PMID: 34812547, PMCID: PMC8810588, DOI: 10.1002/mrm.29097.Peer-Reviewed Original ResearchMeSH KeywordsHeartHumansImage Interpretation, Computer-AssistedMagnetic Resonance ImagingPhantoms, ImagingReproducibility of ResultsConceptsFlip-angle estimationCardiac T<sub>1</sub> mappingGradient echo readoutThrough-plane spatial resolutionImaging timePractical imaging timesFree breathingPhantom studyB1 correctionAccelerated imagingIn-planeT)-spaceMyocardial T<sub>1</sub> valuesSubspace-based methodsSpatial resolutionImaging experimentsAcquisition schemeT)-space dataSubject-specific timeCorrectionModified Look-Locker inversion recoveryLook-Locker inversion recoveryTime of data acquisitionAverage imaging timeInversion-recovery sequenceHigh-Resolution Label-Free Molecular Imaging of Brain Tumor
Guo R, Ma C, Li Y, Zhao Y, Wang T, Li Y, Fakhri G, Liang Z. High-Resolution Label-Free Molecular Imaging of Brain Tumor. Annual International Conference Of The IEEE Engineering In Medicine And Biology Society (EMBC) 2021, 00: 3049-3052. PMID: 34891886, DOI: 10.1109/embc46164.2021.9630623.Peer-Reviewed Original ResearchConceptsMagnetic resonance spectroscopic imagingBrain tumorsIntra-tumoural metabolic heterogeneityAssessment of treatment efficacySmall-sized tumorsClinical applicationN-acetyl aspartateBrain tumor characterizationPotential clinical applicationsApplication of magnetic resonance spectroscopic imagingTumor characterizationMolecular imaging techniquesBrain metabolitesImaging of brain tumorsTumorTreatment efficacyClinical relevanceMetabolic imagingDiagnosed brain tumorsHigh-resolution metabolic imagingMetabolic heterogeneityTumor detectionMolecular imaging of brain tumorsLabel-free molecular imagingLabel-free molecular imaging technique4D magnetic resonance imaging atlas construction using temporally aligned audio waveforms in speech
Xing F, Jin R, Gilbert I, Perry J, Sutton B, Liu X, Fakhri G, Shosted R, Woo J. 4D magnetic resonance imaging atlas construction using temporally aligned audio waveforms in speech. The Journal Of The Acoustical Society Of America 2021, 150: 3500-3508. PMID: 34852570, PMCID: PMC8580575, DOI: 10.1121/10.0007064.Peer-Reviewed Original ResearchConceptsAudio waveformTemporal domain informationMulti-subject dataAtlas constructionMutual information measureMR image datasetsImage datasetsTarget domainDomain informationPost-processing methodImage sequencesTemporal alignmentSpatiotemporal alignmentMatching patternsInformation measuresImage dataSquare errorAligned volumesAlignment mapOverall score increaseMR technologyCross-correlationDeformable registrationSpeechImagesNeurovascular imaging with QUTE-CE MRI in APOE4 rats reveals early vascular abnormalities
Leaston J, Ferris C, Kulkarni P, Chandramohan D, van de Ven A, Qiao J, Timms L, Sepulcre J, Fakhri G, Ma C, Normandin M, Gharagouzloo C. Neurovascular imaging with QUTE-CE MRI in APOE4 rats reveals early vascular abnormalities. PLOS ONE 2021, 16: e0256749. PMID: 34449808, PMCID: PMC8396782, DOI: 10.1371/journal.pone.0256749.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApolipoprotein E4Blood-Brain BarrierBrainDisease Models, AnimalGene Knock-In TechniquesHumansMagnetic Resonance ImagingRatsConceptsVascular abnormalitiesAPOE-e4Contrast-enhanced magnetic resonance imagingBlood-brain-barrier leakageNeurovascular dysfunctionSmall vessel abnormalitiesMagnetic resonance imagingTri-synaptic circuitBlood-brain-barrierCross-sectional studyFemale ratsSignificant signal increaseHyper-vascularizationCerebrovascular abnormalitiesVessel abnormalitiesNeurovascular imagingQUTE-CEBrain volumeAnimal modelsPathological causesAbnormalitiesHistological validationImaging modalitiesResonance imagingA deep joint sparse non-negative matrix factorization framework for identifying the common and subject-specific functional units of tongue motion during speech
Woo J, Xing F, Prince J, Stone M, Gomez A, Reese T, Wedeen V, El Fakhri G. A deep joint sparse non-negative matrix factorization framework for identifying the common and subject-specific functional units of tongue motion during speech. Medical Image Analysis 2021, 72: 102131. PMID: 34174748, PMCID: PMC8316408, DOI: 10.1016/j.media.2021.102131.Peer-Reviewed Original ResearchConceptsNon-negative matrix factorizationSparse Non-negative Matrix FactorizationIterative shrinkage-thresholding algorithmNon-negative matrix factorization frameworkDeep neural networksMatrix factorization frameworkDeep learning frameworkTongue motionIdentified functional unitsGraph regularizationClustering performanceWeight mapLearning frameworkSpectral clusteringNeural networkMatrix factorizationModular architectureIncreased interpretabilityMotion dataFactorization frameworkConvoluted natureComparison methodTagged magnetic resonance imagingMuscle coordination patternsSpeechMagnetic resonance parameter mapping using model‐guided self‐supervised deep learning
Liu F, Kijowski R, Fakhri G, Feng L. Magnetic resonance parameter mapping using model‐guided self‐supervised deep learning. Magnetic Resonance In Medicine 2021, 85: 3211-3226. PMID: 33464652, PMCID: PMC9185837, DOI: 10.1002/mrm.28659.Peer-Reviewed Original ResearchMeSH KeywordsArtifactsDeep LearningImage Processing, Computer-AssistedMagnetic Resonance ImagingMagnetic Resonance SpectroscopyConceptsMR parameter mappingSupervised learningReconstruction qualityImaging modelSelf-supervised deep learningStandard supervised learningConventional iterative reconstructionData setsDeep learning purposesSuperior reconstruction qualityImprove reconstruction qualityQuantitative MRI applicationsUndersampled k-spacePresence of noisePhysical modeling constraintsSparsity constraintNetwork trainingReconstruction performanceDeep learningReconstruction frameworkMap extractionImprove image qualitySuppress noiseGround truthUndersampling artifacts
2020
Motion correction for PET data using subspace-based real-time MR imaging in simultaneous PET/MR
Marin T, Djebra Y, Han P, Chemli Y, Bloch I, Fakhri G, Ouyang J, Petibon Y, Ma C. Motion correction for PET data using subspace-based real-time MR imaging in simultaneous PET/MR. Physics In Medicine And Biology 2020, 65: 235022. PMID: 33263317, PMCID: PMC7985095, DOI: 10.1088/1361-6560/abb31d.Peer-Reviewed Original ResearchMeSH KeywordsArtifactsHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMovementMultimodal ImagingPositron-Emission TomographyTime FactorsConceptsPositron emission tomography reconstructionMotion-corrected PET reconstructionsPET reconstructionMotion-corrected PET imagesIrregular respiratory motionMotion fieldMotion correction methodMotion correction approachIrregular motion patternsUndersampled k-space dataImage quality of positron emission tomographyQuality of positron emission tomographyMotion patternsLow-rank characteristicsRespiratory motionContrast-to-noise ratioEstimated motion fieldSurrogate signalsMotion correctionK-space dataImage qualityReal-time MR imagingSimultaneous PET/MRMotion artifact reductionPET/MR scannersPositron annihilation localization by nanoscale magnetization
Gholami Y, Yuan H, Wilks M, Josephson L, El Fakhri G, Normandin M, Kuncic Z. Positron annihilation localization by nanoscale magnetization. Scientific Reports 2020, 10: 20262. PMID: 33219274, PMCID: PMC7680104, DOI: 10.1038/s41598-020-76980-9.Peer-Reviewed Original ResearchConceptsNanoscale magnetsSpatial resolution of PET imagesImproved dose localizationPositron emitting sourcesResolution of PET imagesPositron emission tomography instrumentationSpatial resolutionPositron emission tomographyAnnihilation quantaPhoton pairsPositron rangeDose localizationPositron annihilationCharged particlesOrtho-positroniumAnnihilationSuperparamagnetic iron oxide nanoparticlesCancer theranostic strategyPositron emission tomography scanPositronElectronic placesImage blurringPET imagingPET-MRITreatment outcomesAttenuation correction using deep Learning and integrated UTE/multi-echo Dixon sequence: evaluation in amyloid and tau PET imaging
Gong K, Han P, Johnson K, El Fakhri G, Ma C, Li Q. Attenuation correction using deep Learning and integrated UTE/multi-echo Dixon sequence: evaluation in amyloid and tau PET imaging. European Journal Of Nuclear Medicine And Molecular Imaging 2020, 48: 1351-1361. PMID: 33108475, PMCID: PMC8411350, DOI: 10.1007/s00259-020-05061-w.Peer-Reviewed Original ResearchMeSH KeywordsDeep LearningHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMultimodal ImagingPositron-Emission TomographyTomography, X-Ray ComputedConceptsAttenuation correctionResultsThe Dice coefficientPseudo-CT imagesMR-based AC methodsAccurate ACAC accuracyPET imagingDice coefficientQuantitative accuracyAtlas methodAC methodGradient echoNear verticesTau imagingTau PET imagingAlzheimer's diseaseUltrashortCorrectionTau pathologyRapid acquisitionDeep learning methodsMonitoring of Alzheimer’s diseasePET/MRAmyloidHigh-performance rapid MR parameter mapping using model-based deep adversarial learning
Liu F, Kijowski R, Feng L, El Fakhri G. High-performance rapid MR parameter mapping using model-based deep adversarial learning. Magnetic Resonance Imaging 2020, 74: 152-160. PMID: 32980503, PMCID: PMC7669737, DOI: 10.1016/j.mri.2020.09.021.Peer-Reviewed Original ResearchMeSH KeywordsBrainDeep LearningHumansImage Processing, Computer-AssistedKneeMagnetic Resonance ImagingTime FactorsConceptsConvolutional neural networkMR parameter mappingAdversarial learningState-of-the-art reconstruction methodsEnd-to-end convolutional neural networkUndersampled k-space dataConvolutional neural network approachAdversarial learning approachState-of-the-artStructural similarity indexImage reconstruction frameworkEnd-to-endImage sharpnessData consistencyConventional reconstruction approachesReconstruction approachK-space dataImprove image sharpnessImage reconstruction approachEstimated parameter mapsImage sparsityTexture restorationNetwork trainingImage datasetsReconstruction performanceAccelerated J‐resolved 1H‐MRSI with limited and sparse sampling of (‐space
Tang L, Zhao Y, Li Y, Guo R, Clifford B, Fakhri G, Ma C, Liang Z, Luo J. Accelerated J‐resolved 1H‐MRSI with limited and sparse sampling of (‐space. Magnetic Resonance In Medicine 2020, 85: 30-41. PMID: 32726510, PMCID: PMC7992196, DOI: 10.1002/mrm.28413.Peer-Reviewed Original ResearchMR‐based PET attenuation correction using a combined ultrashort echo time/multi‐echo Dixon acquisition
Han P, Horng D, Gong K, Petibon Y, Kim K, Li Q, Johnson K, Fakhri G, Ouyang J, Ma C. MR‐based PET attenuation correction using a combined ultrashort echo time/multi‐echo Dixon acquisition. Medical Physics 2020, 47: 3064-3077. PMID: 32279317, PMCID: PMC7375929, DOI: 10.1002/mp.14180.Peer-Reviewed Original ResearchMeSH KeywordsHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingPhantoms, ImagingPositron-Emission TomographyTomography, X-Ray ComputedConceptsLinear attenuation coefficientPositron emission tomography attenuation correctionPhysical compartmental modelAttenuation correctionShort T<sub>2</sub> componentPET attenuation correctionRadial k-space trajectoryMagnetic resonance (MR)-based methodK-space trajectoriesRadial trajectoryK-spaceAttenuation coefficientDixon acquisitionsPositron emission tomographyWhole white matterMuting methodImage reconstructionImaging speedMR signalMRAC methodPositron emission tomography imagingCorrectionGray matter regionsPhantomMatter regions