Visualisation of Large-Scale Brain Networks
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VisualisationofLarge-ScaleBrainNetworksAlleMeijeWink,SophieAchard,JohnSucklingandEdBullmoreBrainMappingUnit,DepartmentofPsychiatry,Addenbrooke’sHospital,UniversityofCambridge,UnitedKingdom{amw71,sa428,js369,etb23}@cam.ac.uk
ObjectiveAnalysisofnetworkpropertiesinresting-statefMRIexperiments[1]demonstratethepossi-bilitytoinvestigatelargenumbersofveryweakconnectionsbetweenregionsthatarenotrelatedtoanytask.However,inbrainnetworks,thegoalisoftentofindthespatiallocationandextentofasignalsource.Thisstudyusesthree-dimensional(3D)visualisationtech-niques(e.g.surfacerendering)andgraphicsprimitives(surfaces,lines,tubes)todisplaytheconnectionsofabrainnetwork,aswellastheregionsthatareconnected,inanatomicalspace.
TheoryOtheranalysesoflargeresting-statenetworks[2,3]showthatlargenetworkswithdifferenttypesofconnections(long-range,lowfrequencyvs.short-range,high-frequency)presentavisualisationproblem:thelargeamountofdatacallsforanabstractpresentationthatreor-ganisesthelocationsofthenodes[4],orsimplifiedrepresentationswherepartofthespatialinformationisdiscarded([3],seeFig.5-6).
asurfacerenderingoftheAALregionsImaging5healthyvolunteerswerescannedonaBrukerMedSpec3Tsystemwhiletheywerely-ingstillwiththeireyesclosed.Scanningparameterswere:EPIsequence,TR1.1s,2048scans.Region-meantimeserieswereextractedusingtheAALregions[5],seefigure1.Awavelet-covariancealgorithmwasusedtocomputethecovariancematricesbetweentheregion-meantimesignalsondifferenttimescales.Ontimescale4(0.03-0.06Hz),therearebothlong-rangeandshort-rangeconnections.Theconnectionstrengthswereaveragedacrosssubjects.
ProcessingpipelineWeusedsurfacerenderingtoproduceasemi-transparent3Dcontourofasmoothedandthresholdedtemplateimage.Thissurface,whichisinthesamespaceastheAALimage,providedtheanatomicallandmarksfortheconnectionsbetweenbrainregions.Thenetworkwasgivenasatextfileof90lines(90regionswereexamined;e.g.Thecerebellumwasnotincluded).Eachline,readbyascript,describedtheconnectionsofeachregiontootherregions.Theseconnectionswerepresentedascolouredtubes,withdifferentcoloursforlong-rangeconnections(blue,thick)andshort-rangeconnections(red,thin).ThepipelinewasimplementedinasaTclscript(www.tcl.tk),usingTclwrappersoftheVisualizationToolkitclasses(www.vtk.org).
vtkStructuredPointsReadervtkMarchingCubesvtkSmoothPolyDataFiltervtkTriangleFiltervtkDecimatevtkTubeFilter (colour, size)vtlCellArray (connections)vtkPolyData (spatial links)3D image dataMNI templateread connectivity matrixread connectivity matrixvtkRenderWindowvtkRenderervtkCameravtkPolyDataMappervtkActorvtkPolyDataMappervtkActorvtkVRMLExporterget centroid coordinatesTcl Scriptconnectionsconnectionsmatrix: longmatrix: shortvtkPoints (centroids)vtkTubeFilter (colour, size)vtlCellArray (connections)vtkPolyData (spatial links)
vtkPolyDataMappervtkActor
Theprocessingpipeline,asimplementedinTcl/VTKThispresentation,whichcanbefreelyrotatedonacomputerscreen,clearlyshowsnetworksintheoccipitalandprefrontalcorticesthataredominatedbyshort-rangeconnections,whiletherestofthebrainshowsmanylong-rangeconnections.Theseconnectionsareanterior-posterior,aswellassuperior-inferiorandbilateral.
differentconnectiontypesshowninanatomicalspaceusingasemitransparentsurfaceandcolouredtubes
TheVRMLexporterofVTKwasusedtocreatearepresentationofthe3Dmodelthatotherprogramscanread.Thisgivesresearchersextrapossibilitiestoexchangetheirfindings.
ConclusionTheinteractive3Dvisualisationmethodpresentedheregivesquickinsightintothelocation,strength,andspanofbrainconnections.Withotherextensions(e.g.interactiveuseoftheshapeofconnectedregions,cutsurfaces)thismaybeaninvaluabletoolfortheevaluationoffunctionalneuroimagingexperimentsattheconnectionslevel.
References[1]S.Achardetal.(2005)AResilient,Low-Frequency,Small-WorldHumanBrainFunctionalNetworkwithHighlyConnectedAssociationCorticalHubs,J.Neurosci16(1):63-72.
[2]R.S.Salvadoretal.(2005)NeurophysiologicalArchitectureofFunctionalMagneticRes-onanceImagesofHumanBrain,CerebralCortex.15(9):1332-1342.
[3]R.S.Salvadoretal.(2005)Undirectedgraphsoffrequency-dependentfunctionalconnec-tivityinwholebrainnetworks,Phil.Trans.RoySoc.B360(1457):937-946.
[4]Strogatz(2001)Exploringcomplexnetworks,Nature410(6825):268-276.[5]N.Tzourio-Mazoyeretal.(2002)AutomatedanatomicallabelingofactivationsinSPMusingamacroscopicanatomicalparcellationoftheMNIMRIsingle-subjectbrain,Neu-roimage15(1):273-289.
poster761M-AM,HBM2005,HumanBrainMapping,June12–16,2005,Toronto,CanadasponsoredbytheNIHHumanBrainproject