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Chapter4TheImagedBrain
March10,2016
5707BrainandCognitiveScience
MethodsforBrainandCognitiveScience
Electrophysiology:Electroencephalography(EEG)Magnetoencephalography (MEG)Transcranial magneticstimulation(TMS)
Neuroimaging:MagneticResonanceImaging(MRI)functionalMRI(fMRI)Positronemissiontomography(PET)
Chapter3ElectrophysiologicalBrain
Chapter4ImagedBrain
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PaulBroca (1824 1880):Tansbrain
Apatient,withlossofspeechwastransferredtoPaulBrocas care LosttheabilitytospeakexceptforTan. Goodcomprehension Braindamagetothelefthemisphere.
CarlWernicke (1848 1904)
Reported acaseofawomanwithdisruptedbutfluentspeech (1874)Fluentbutmeaningless speechComprehension isimpairedBraindamagetothelefthemisphere
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Leftsideofthebrain
Arcuatefasciculus:connectionbetweenBrocas areaandWernickesarea
Outlinefortoday
Thebasicconceptofimages Structural/anatomicalbrainimagingtechniquesCT/structuralMRI/DiffusionMRIPrincipleApplications
Functionalbrainimagingtechniques TaskrelatedfunctionalMRI(taskfMRI)PrincipleExperimentaldesignApplications
RestingstatefunctionalMRI(rsfMRI)andgraphtheory
6
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Outlinefortoday
Thebasicconceptofimages Structural/anatomicalbrainimagingtechniquesCT/structuralMRI/DiffusionMRIPrincipleApplications
Functionalbrainimagingtechniques TaskrelatedfunctionalMRI(taskfMRI)PrincipleExperimentaldesignApplications
RestingstatefunctionalMRI(rsfMRI)andgraphtheory
7
Thebasicconceptofimages
Beforeanyimageprocessing,weneedtounderstandtheformatoftheimage.
Neuralimagesaredigitalimages.
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Resolutionofanimage
lowresolution highresolution
Thebasicconceptofimages
Whatistheformatoftheimage? digitalimages
Adigitalimage=Amatrixofnumbers,w/onenumberrepresentsonepixel
Pixel =Pictureelement Adigitalimage=Amathematicalmatrix
222 220 200 146 103
200 158 127 96 73
207 131 103 82 86
202 126 112 124 133
PixelValues(p)
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Columns(j)
Rows(i)
Pixel Datap(i,j)
Thebasicconceptofimages
PixelsandImageMatrices numbersofpixels=numberofrows* numberofcolumns
Frommathematicstophysics
Adigitalimage=amathematicalmatrix Apixelinthematrixhasaphysicaldimension(e.g.mm)
1024x1024 64x64 32x32 16x16
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Frommathematicstophysics
Adigitalimage=amathematicalmatrix Apixelinthematrixhasaphysicaldimension(e.g.mm)
8mm 4mm 2mm 1.5mm 1mm
Outlinefortoday
Thebasicconceptofimages Structural/anatomicalbrainimagingtechniquesCT/structuralMRI/DiffusionMRIPrincipleApplications
Functionalbrainimagingtechniques TaskrelatedfunctionalMRI(taskfMRI)PrincipleExperimentaldesignApplications
RestingstatefunctionalMRI(rsfMRI)andgraphtheory
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Computedtomography(CT)
ProjectionoftheXrayfrommultipleangles 3Dimagesbasedontissuedensity
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Outlinefortoday
Thebasicconceptofimages Structural/anatomicalbrainimagingtechniquesCT/structuralMRI/DiffusionMRIPrincipleApplications
Functionalbrainimagingtechniques TaskrelatedfunctionalMRI(taskfMRI)PrincipleExperimentaldesignApplications
RestingstatefunctionalMRI(rsfMRI)andgraphtheory
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Necessaryequipment:3TeslaMRIscanner
Magnet
Gradientcoil
RFcoil
http://www.magnet.fsu.edu/education/tutorials/magnetacademy/mri/fullarticle.html
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WhatdoesanMRIscansoundlike
HighresolutionT1structuralMRIimages
graymatter(morewater)
whitematter(morefat)
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3TMRIscandemohttps://www.youtube.com/watch?v=Gs3onhjuKio
Magnet
Earthsmagneticfield=0.5Gauss
1Tesla=10,000Gauss 3Tesla(T)=
3X10,000/0.5=60,000Earthsmagneticfield
Permanent Superconducting Activeshielding
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Review:Magneticfield
GradientCoil
Gradientstrength Activeshielding Shimming
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Radiofrequency(RF)coil
Transmission Receiving Severalkindsofcoils:
ActivecoilsPassivecoilsBirdcagecoils
MRIsafety
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MRIsafetyvideoIhttp://www.youtube.com/watch?v=6BBx8BwLhqg&feature=related
MRIsafetyvideoII
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https://www.youtube.com/watch?v=5KuzTyn45og
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Subjectsafety
Anyonegoingnearthemagnet subjects,staffandvisitors mustbethoroughlyscreened
Subjectsmusthavenometalintheirbodies:pacemaker aneurysmclipsmetalimplants(e.g.,cochlearimplants) somedentalwork(fillingsokay)
Subjectsmustremovemetalfromtheirbodies jewellery,watch,piercings,coins,etc.wallet anymetalthatmaydistortthefield
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fmri
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MagneticResonanceImaging(MRI)
MRI=NMR+Imaging Magnetic:Magnetizationinducedbymagneticfield
Resonance:Exciteandreceiveofmagnetization
Imaging:Spatialencodingofmagnetization()
MRImeasures
Differenttissueinthebrain(e.g.,graymatter,whitematter)
Differenttissuehasdifferentwatercontent Watercontainshydrogenatoms(H20)
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Magnetizationinducedbymagneticfield
+ =()(spin)
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MRIsignalvariesacrosstissue
Time
Signalintensity
TissueA(e.g.,fat)
TissueB(e.g.,water)
HighresolutionT1structuralMRIimages
graymatter(morewater)
whitematter(morefat)
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Structuralimaging
CT T1MRIimage T2MRIimage
Howtomeasurethedifferencesbetweengroups?
Normalyoungadult(mid20s)
Normalolderadult(late70s)
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Voxelbasedmorphometry analysis(VBM)
voxelwisecomparisonofthelocalvolumeofgraymatterandwhitematterbetweentwogroupsofsubjects
StructuralMRI:Voxelbasedmorphometry analysis(VBM)
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StructuralMRIapplication:IQandcorticaldevelopment
StructuralMRIapplication:IQandcorticaldevelopment
Moreintelligentchildrendemonstrateaparticularlyplasticcortex,withaninitialacceleratedandprolongedphaseofcorticalincrease:theneuroanatomicalexpressionofintelligenceinchildrenisdynamic
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StructuralMRIapplication:Learningandmemory
Changesingraymatterinducedbytraining: StudentsinexperienceatjugglingDividedintotwogroups(scanthem)Onegroupspracticesjugglingfor3months,andtheotherdoesnt(scanagain)
Wait3months,noonejuggles(scanagain)
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StructuralMRIapplication:Learningandmemory
LargerposteriorhippocampusinLondontaxidrivers:LondontaxidriverisbetteronspatialnavigationOver26,000streetswithinasixmileradiusofCharing Crossand1,400differentplacesofinterests.
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StructuralMRIapplication:Learningandmemory
LargerposteriorhippocampusinLondontaxidrivers: StructureMRIscan:16licensedLondontaxidriversand50nontaxidrivers.
Outlinefortoday
Thebasicconceptofimages Structural/anatomicalbrainimagingtechniquesCT/structuralMRI/DiffusionMRIPrincipleApplications
Functionalbrainimagingtechniques TaskrelatedfunctionalMRI(taskfMRI)PrincipleExperimentaldesignApplications
RestingstatefunctionalMRI(rsfMRI)andgraphtheory
46
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Restricteddiffusion:AnisotropicdiffusionFractionalAnisotrophy (FA)~1
Freediffusion:IsotropicdiffusionFractionalAnisotrophy (FA)~0
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DiffusionMRI:Diffusiontensorimaging(DTI)
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NeuralfiberreconstructionCalculationofthediffusiontensor
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DiffusionMRI:Diffusiontensorimaging(DTI)
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DTIapplications:sexdifferences
Malebrain Femalebrain
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DTIapplicationsEvolutionofthearcuatefasciculus
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10invivohuman1invivochimpanzee3postmortemchimpanzee1invivomacaque2postmortemmacaque
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Outlinefortoday
Thebasicconceptofimages Structural/anatomicalbrainimagingtechniquesCT/structuralMRI/DiffusionMRIPrincipleApplications
Functionalbrainimagingtechniques TaskrelatedfunctionalMRI(taskfMRI)PrincipleExperimentaldesignApplications
RestingstatefunctionalMRI(rsfMRI)andgraphtheory
53
MRIvs.fMRI
MRI studiesbrainanatomy Functional MRI(fMRI)studiesbrainfunction
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MRIscannerandfMRIscan
ThefirstBrainImagingexperiment
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Vasculatureofhumanbrain
Cerebralmetabolism:neuronalenergyconsumption
fMRIindirectlymeasurebrainfunction
Functionalbrainmaps:mapsofneuralactivity Mapsofneuralactivity:
Imagingthechangeinbloodflow(hemodynamicresponse)relatedtoenergyusebyneurons.
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Oxygenated BloodDeoxygenated Blood
Resting
Active
fMRI:BOLDsignal
BloodOxygenationLevelDependent(BOLD)signal
MRI
Neural
Metabolic
Hemodynamic
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CategoriesoffunctionalMRI
TaskrelatedfMRISpecificexperimentaldesigntoexaminethebrainfunctionsassociatedwithperception,attention,language,learningandmemory,decisionmaking,andemotion.Brainduringwork
RestingstatefMRINospecificexperimentaldesign Brainatrest
CategoriesoffunctionalMRI
TaskrelatedfMRISpecificexperimentaldesigntoexaminethebrainfunctionsassociatedwithperception,attention,language,learningandmemory,decisionmaking,andemotion.Brainduringwork
RestingstatefMRINospecificexperimentaldesign Brainatrest
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taskrelatedfMRI(taskfMRI):Physicaltask
+
1000ms500ms 4 9
+
1000ms500ms 3 3
+Time
...1000ms500ms 2 7
TaskfMRIDatatransformations
Motioncorrection Smoothing
kernel
Spatialnormalization
Standardtemplate
fMRItimeseries
GeneralLinearModel
Designmatrix
Parameterestimates
Gaussianfieldtheory
p
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TaskfMRIresults
TasksfMRIbasic:orientation
Sliceorientation:AP:anteriorposterior()SI:superiorinferior()LR:leftright()
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TaskfMRIbasic:orientation
NeurologicalconventionLeftisleft,rightisright
Radiologicalconvention Leftisright,rightisleft
Makesurehowyoursoftwaredoingwithleft/right Ifyourereallyunsure,tapeavitaminEoroilcapsuletotheonesideofthesubjectshead.Itwillshowupontheanatomicalimage
left
left
right
right
IntroductiontotaskfMRIhttps://www.youtube.com/watch?v=BmQR57V5TVU
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Outlinefortoday
Thebasicconceptofimages Structural/anatomicalbrainimagingtechniquesCT/structuralMRI/DiffusionMRIPrincipleApplications
Functionalbrainimagingtechniques TaskrelatedfunctionalMRI(taskfMRI)PrincipleExperimentaldesignApplications
RestingstatefunctionalMRI(rsfMRI)andgraphtheory
69
Experimentaldesigns
BetweensubjectdesignDifferentconditionsareassignedtodifferentsubjectgroupse.g.malevs.female;drugabuservs.abstainers;youngvs.olderadults.
WithinsubjectdesignEachsubjectparticipantsinallexperimentalconditions
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Essentialcomponentsinanexperimentaldesign
IndependentvariablesManipulatedbytheexperimenterse.g.stimulus(face,words,pictures)
DependentvariableQuantitiesthatmeasuredbyexperimenters
e.g.,heartrate,bloodpressure,cortisollevel,BOLDsignal
e.g.,accuracy,reactiontimes
Variables:
Anterior
PosteriorLOCLOC
Experimentaldesigns Experimentalconditions Containsthestimuliortask
thatismostrelevanttoresearchhypothesis
Taskcondition
Controlconditions Baselinecondition Nontask condition
Experimentalcondition
Controlcondition
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Experimentaldesigns:fMRI
Experimentalconditions Controlconditions
faces Scrambledpicturesw/samespatialfrequency
=
TaskfMRIstudies:theoreticallydriven
Welldefinedproblem
TheoryA PredictionATheoryB PredictionB
Experiment
TheoryAorBstandsorrevisedtheory
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TaskfMRIstudies:theoreticallydriven
Anterior
PosteriorLOCLOC
Differentstimuluscategorieselicitdifferentpatternsofactivityinventralvisualcortex.
Predictions: Facerecognitiontaskleadtoactivationinfusiformfacearea Animacy judgmenttaskleadtoactivationinlateraloccipitalcomplex
Place/HouseAreas(Parahippocampal gyrus)
ObjectAreas(Lateraloccipitalcomplex)
FaceAreas(FusiformFaceArea)
ThreedistinctlevelsofresearchhypothesisintaskfMRIstudies
Hemodynamic
Neuronal
Psychological(Cognitive)
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Confoundingfactors
Anypropertythatcovarieswiththeindependentvariablewithintheconductedexperiment
Couldbedistinguishedfromtheindependentvariablesusingadifferentexperimentaldesign
ExampleofconfoundingCleverHans
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CleverHanseffect:Observerexpectancy
WhenHansisclever WhenHansisnotclever
Confoundingfactors
Anypropertythatcovarieswiththeindependentvariablewithintheconductedexperiment
Couldbedistinguishedfromtheindependentvariablesusingadifferentexperimentaldesign
Evidenceofglobalwarming?
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Topreventconfoundingfactors
Randomizing orCounterbalancingtheorderoftheconditionsmakessurethatthepotentialeffectsaredistributedequallyacrosstheconditionsoftheexperiment. Randomized:ABC,ACB,BCA,BAC,CAB,CBA(N!)
4conditions:24;5conditions:120;6conditions:720
Counterbalancing:ABC,BCA,CABEaseofusage:donthavetoswitchinstructionsorequipmentveryoften
TaskfMRIapplication:Decodingthereadingbrain
Hearingwords:Superior/middletemporalregions
Seeingwords:Leftoccipitotemporalregion
Petersenetal.,1988
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Speaking/producingwords:Motorregion
Generatingwords:Leftinferiorfrontalregion
TaskfMRIapplication:DecodingthereadingbrainPetersenetal.,1988
TaskfMRIapplication:ColorwordStrooptask
Congruent()
Incongruent()
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TaskfMRIapplication:consciousness?
Awarenessinthevegetativestate 23yearoldwomansustainedaseveretraumaticbraininjury Spokeninstructionstoperformtwomentalimagerytasks: imagingplayingagameoftennis imagingvisitingalloftheromofherhouse
Advantages&disadvantagesoffMRI
AdvantagesNoninvasiveSpatialresolutionisgoodShowsallparticipatingareas,notjustcriticalones
DisadvantagesPoortemporalresolutionDifficulttousewithsubjectsandtoobtaingoodmeasurementsSensitivitytoheadmotionPregnancy,obesity,metalparts,etc.
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Aneuralportraitofthehumanmind
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http://is.gd/cpNjvA
Outlinefortoday
Thebasicconceptofimages Structural/anatomicalbrainimagingtechniquesCT/structuralMRI/DiffusionMRIPrincipleApplications
Functionalbrainimagingtechniques TaskrelatedfunctionalMRI(taskfMRI)PrincipleExperimentaldesignApplications
RestingstatefunctionalMRI(rsfMRI)andgraphtheory
88
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CategoriesoffunctionalMRI
TaskrelatedfMRISpecificexperimentaldesigntoexaminethebrainfunctionsassociatedwithperception,attention,language,learningandmemory,decisionmaking,andemotion.Brainduringwork
RestingstatefMRINospecificexperimentaldesign Brainatrest
Restingstatebrainactivity
RestingstatebrainactivityassessedbyfMRINoninvasive,bloodoxygenleveldependent(BOLD)
Defaultmodenetwork(DMN):AsetofbrainregionsshowingincreasedfMRIactivityintaskfreestatecomparedtocognitivelydemandingtaskatrest.deactivationSuperior/middlefrontal,medialprefrontal,posteriorcingulatecortex(PCC)/precuneus,superiorparietal,hippocampalregion.
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Defaultmodenetwork(DMN)&Taskrelatedactivationregions
Parketal.,2010
Young
rsfMRIapplication:mindwandering
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rsfMRIapplication:mindwandering
CorrelationbetweenmindwanderingfrequencyandBOLDchange
Smallworld:Graphtheory
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Smallworld:Graphtheory
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WhatisrestingstatefMRI?
96Adaptedfrom,2015
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Functionalneuralconnectivity:restingstatefunctionalMRI
Stronglycorrelatedpatternsofbrainactivityamongdistantbrainregions(i.e.,functionalconnectivity)aretakenasanindicationthattheseregionscommunicate.
Functionalconnectivityisoftenmeasuredasinterregionalcorrelationsamongspontaneousfluctuationsofhemodynamicactivityduringarestingstate whileparticipantsliepassivelyintheMRImachine,butnoactivecognitiveorbehavioraldemandsareimposed.
Dosenbach etal.,2008
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Outlinefortoday
Thebasicconceptofimages Structural/anatomicalbrainimagingtechniquesCT/structuralMRI/DiffusionMRIPrincipleApplications
Functionalbrainimagingtechniques TaskrelatedfunctionalMRI(taskfMRI)PrincipleExperimentaldesignApplications
RestingstatefunctionalMRI(rsfMRI)andgraphtheory
100