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NationalAllianceforMedicalImageComputingAnnualResearchProgressReport2007

Contents

1Introduction.............................................................................................. 2372FourMainThemes................................................................................... 2382.1DiffusionImageAnalysis....................................................................... 2392.2StructuralAnalysisTheme..................................................................... 2432.3FunctionalMRIAnalysisTheme........................................................... 2472.4NAMICKitTheme................................................................................. 2493Highlights.................................................................................................. 2524ImpactandValuetoBiocomputing..................................................... 2545NAMICTimeline................................................................................... 255AppendixA:Publications 266AppendixB:EABReport 275

NATIONALALLIANCEFORMEDICALIMAGECOMPUTINGTHIRDANNUALRESEARCHPROGRESSREPORT

20071 IntroductionTheNationalAllianceforMedicalImagingComputing(NAMIC)isnowinitsthirdyear.ThisCenteriscomprisedofamultiinstitutional,interdisciplinaryteamofcomputerscientists,softwareengineers,andmedicalinvestigatorswhohavecometogethertodevelopandapplycomputationaltoolsfortheanalysisandvisualizationofmedicalimagingdata.AfurtherpurposeoftheCenteristoprovideinfrastructureandenvironmentalsupportforthedevelopmentofcomputationalalgorithmsandopensourcetechnologies,andtooverseethetraininganddisseminationofthesetoolstothemedicalresearchcommunity.Thedrivingbiologicalprojects(DBPs)forthefirstthreeyearsoftheCentercamefromschizophrenia,althoughthemethodsandtoolsdevelopedareclearlyapplicabletomanyotherdiseases.

Inthefirstyearofthisendeavor,ourmainfocuswastodevelopalliancesamongthemanycorestoincreaseawarenessofthekindsoftoolsneededforspecificimagingapplications.OurfirstannualreportandAllhandsmeetingreflectedthisemphasisoncores,whichwasnecessarytobringtogethermembersofaninterdisciplinaryteamofscientistswithsuchdiverseexpertiseandinterests.InthesecondyearoftheCenterouremphasisshiftedfromtheintegrationofcorestotheidentificationofthemesthatcutacrosscoresandweredrivenbytherequirementsoftheDBPs.Wesawthisshiftasanaturalevolution,giventhatthedevelopmentandapplicationofcomputationaltoolsbecamemorecloselyalignedwithspecificclinicalapplications.ThischangeinemphasiswasreflectedintheCentersfourmainthemes,whichincludedDiffusionTensorAnalysis,StructuralAnalysis,FunctionalMRIAnalysis,andtheintegrationofnewlydevelopedtoolsintotheNAMICToolKit.InthethirdyearoftheCenter,collaborativeeffortshavecontinuedalongeachofthesethemesamongcomputerscientists,clinicalcorecounterparts,andengineeringpartners.Wearethusquitepleasedwiththefocusonthemes,andwealsonotethatnotonlyhasourprogresscontinuedbutalsomoreprojectshavecometofruitionwithrespecttopublicationsandpresentationsfromNAMICinvestigators,whicharelistedonourpublicationspage.

Below,inthenextsection(Section2),wesummarizeourprogressoverthelastyearusingthesamefourcentralthemestoorganizetheprogressreport.ThesefourthemesincludeDiffusionImageAnalysis(Section2.1),StructuralAnalysis(Section2.2),FunctionalMRIAnalysis(Section2.3),andtheNAMICtoolkit(Section2.4).Section3highlightsfourimportantaccomplishmentsofthethirdyear:advancedalgorithmdevelopmentinShapeandDTIanalysis,thenewlyarchitectedopensourceapplicationplatform,Slicer3,andouroutreachandtechnologytransferefforts.Section4summarizestheimpactandvalueofourworktothebiocomputingcommunityatthreedifferentlevels:withinthecenter,withintheNIHfundedresearchcommunity,andexternallytoanationalandinternationalcommunity.Thefinalsectionofthisreport,Section5,providesatimelineofCenteractivities.

Inaddition,theendofthefirstthreeyearsoftheCentermarksatransitionfromthefirstsetofDBPsthatwerefocusedentirelyonschizophreniatoanewsetthatspansawiderrangeofbiologicalproblems.ThenewDBPscontinuetoincludeneuropsychiatricdisorderssuchassystemiclupuserythematosis(MINDInstitute,UniversityofNewMexico),schizophrenia(Harvard),andautism(UniversityofNorthCarolina,ChapelHill),andadditionallyadoptadirectionthatisnewbutsynergisticforNAMIC:prostateinterventions(JohnsHopkinsUniversity).FundingforthesecondroundofDBPsstartsinthenextcycle,butthePIswereabletoattendtherecentAllhandsmeetingandstartdevelopingplansfortheirfutureresearchinNAMIC.

Finally,wenotethatCore3.1(ShentonandSaykin)isintheprocessofapplyingforaCollaborativeR01toexpandcurrentresearchwithNAMIC,whichendsonJuly31,2007.BothDrs.ShentonandSaykinhaveworkedforthreeyearstodrivetooldevelopmentforshapemeasures,DTItools,andpathanalysismeasuresforfMRIaspartofthedrivingbiologicalprojectinNAMIC.TheynowplantoexpandthisresearchinaCollaborativeR01workingcloselywithDrs.Westin,Miller,Pieper,andWells,todesign,assess,implement,andapplytoolsthatwillenabletheintegrationofMRI,DTI,andfMRIinindividualsubjects.TheywillalsodevelopanatlasoffunctionalnetworksandcircuitsthatarebasedonaDTIatlas(i.e.,structuralconnectivity),whichwillbeintegratedwithanetworkoffunctionalconnectivitythatwillbeidentifiedfromfMRIprobesofattention,memory,emotion,andsemanticprocessing.Wementionthisherebecausethiswillbe,toourknowledge,thefirstDBPtoapplyforfurtherfundingtocontinuecriticalworkbegunwithNAMIC.(PleasenotethatthisreportisavailableontheNAMICwikiatthefollowingurl:http://www.namic.org/Wiki/index.php/2007_Annual_Scientific_Report) 2 FourMainThemesThisyearsactivitiesfocusonfourmainthemes:DiffusionImageAnalysis,StructuralAnalysis,FunctionalMRIAnalysis,andtheNAMICKit.Eachofthefollowingsectionsbeginswithanoverviewofthetheme,providesaprogressupdateandlistofkeyinvestigators,andconcludeswithasetoflinkstoadditionalinformationforindividualprojectsinthattheme.

Thesethematicactivitiesinvolvescientistsfromeachofthe7NAMICcores(Appendix).

Core1AlgorithmsRossWhitakerPIhttp://www.namic.org/Wiki/index.php/Algorithm:Main

Core2EngineeringWillSchroederPIhttp://www.namic.org/Wiki/index.php/Engineering:Main

Core3DrivingBiologicalProblemsDBP1MarthaShentonPI/DBP2AndySaykinPI/DBP3StevenPotkinPIhttp://www.namic.org/Wiki/index.php/DBP:Main

Core4ServiceWillSchroederPIhttp://www.namic.org/Wiki/index.php/Service:Main

http://www.na-mic.org/Wiki/index.php/2007_Annual_Scientific_Reporthttp://www.na-mic.org/Wiki/index.php/Algorithm:Mainhttp://www.na-mic.org/Wiki/index.php/Engineering:Mainhttp://www.na-mic.org/Wiki/index.php/DBP:Mainhttp://www.na-mic.org/Wiki/index.php/Service:Main

Core5TrainingRandyGollubPI

http://www.namic.org/Wiki/index.php/Training:Main Core6DisseminationTinaKapurCoPI;StevePieperCoPI

http://www.namic.org/Wiki/index.php/Dissemination:Main Core7LeadershipRonKikinis

http://www.namic.org/Wiki/index.php/Leadership:Main

2.1 DiffusionImageAnalysisTheme

Progress

Overthepastyear,wehavecontinuedtodevelopanumberoftoolsrelevanttodiffusiontensorestimation,fibertractography,andgeometricandstatisticaldiffusiontensoranalysis.Someofthesetoolshavealreadybeenintegratedintodiffusiondedicatedsoftware(e.g.,FiberViewerUNC)andintotheSlicerplatform.Variousgroupsfocusonmoresophisticatedmethodologiesasalternativestoconventionaltractographyformorerobustextractionoffiberbundles(GeorgiaTech,Utah).Otherscombinetractographyresultsfromindividualsintofiberclusteratlases(MIT).Inaddition,UNCstarteddevelopingbrainmappingtoolsforgroupdataanalysis,suchaswhitematteratlasesandtoolsfordataintegration,thatwouldcombineandinterfaceamongdifferentimagingmodalities(suchasstructural,fMRI,andDTI)tobetterestimateanatomicalandfunctionalconnectivity.ThecurrentreportingperiodisclearlycharacterizedbyasignificantlyimprovedefforttowardsapplicationofNAMICDTItoolsdevelopedbyCore1partnerstoclinicaldataprovidedbyCore3DBPsusedinmultipleclinicalprojectsinvolvingseveralpsychiatricpopulations.Belowweprovidedetailedprogressintheareaofdiffusionimageanalysis.

FiberTractExtractionandAnalysis

Sincelastyear,allofthealgorithmsforfibertractographyandanisotropyestimationhavebeenimplementedinboththeFiberViewerandSlicerpackages,andnowtheresultingmethodsarebeingappliedtoclinicalstudies.TheFiberViewertoolanditsapplicationinalargeclinicalUNCDTIstudyhavebeenpublishedinjournals.UtahrecentlyextendedthetractographybasedconceptwithanewapproachbasedonsolvingaPDE,thusreplacingthetractographybasedextractionoffiberbundlesbyafullyvolumetricprocess.Characterizationofbundlesisthenapproachedbyanewregressionmethod(IPMI07).Inasimilarspirit,theBWH/MIT/UNCgroupsapplieddiffusionmeasuresalongaspecificfiberbundleofinerest,parametrizedbyarclength,tothecingulumbundle.GeorgiaTechdevelopsamethodcalledFinslerActiveContourDWI,amathematicallymoresophisticatedapproachtostandardtractographymethodsthatmakesuseofFinslergeometryandsolvesanewanisotropicenergyfunctionforextractionof3Dcurvesfromtensordata.

http://www.na-mic.org/Wiki/index.php/Training:Mainhttp://www.na-mic.org/Wiki/index.php/Dissemination:Mainhttp://www.na-mic.org/Wiki/index.php/Leadership:Main

PreliminaryapplicationstothecinculumbundleinthePNLschizophreniadatasetofourCore3partnerareverypromising.

Inadditiontoclinicalstudies,teamshavebeenworkingonothermethodstodefineandestimatebrainconnectivity.Themostimportantdevelopmentsinthisregardincludevolumetricconnectivityandstochastictractographymeasures.Forvolumetricconnectivity,aPDEbasedapproachtowhitematterconnectivityfromDTIhasbeendeveloped.Thisapproachisfoundedontheprincipalofminimalpathsthroughthetensorvolume.Thismethodcomputesavolumetricrepresentationofawhitemattertractgiventwoendpointregions.Inaddition,statisticalmethodsforquantifyingthefulltensordataalongthesepathwayshavebeenalsodeveloped.DirectionalPDEbasedflowshavebeenproposedandimplementedforasimilarpurpose.Further,anapproachcalledstochastictractography,hasbeendevelopedtocalculatetheprobabilityoftworegionsbeingconnectedbythefibertract.Thisshou