Neuroinformatics for Neuropsychology PDF
Preview Neuroinformatics for Neuropsychology
Vinoth Jagaroo Neuroinformatics for Neuropsychology 123 Neuroinformatics for Neuropsychology Vinoth Jagaroo Neuroinformatics for Neuropsychology 123 VinothJagaroo DepartmentofCommunicationSciences &Disorders EmersonCollege 120BoylstonStreet Boston,MA02116 USA [email protected] and DepartmentofPsychiatryandthe BehavioralNeuroscienceProgram BostonUniversitySchoolofMedicine 715AlbanyStreet Boston,MA02118 USA [email protected] ISBN978-1-4419-0059-3 e-ISBN978-1-4419-0060-9 DOI10.1007/978-1-4419-0060-9 SpringerDordrechtHeidelbergLondonNewYork LibraryofCongressControlNumber:2009930050 ©SpringerScience+BusinessMedia,LLC2009 Allrightsreserved.Thisworkmaynotbetranslatedorcopiedinwholeorinpartwithoutthewritten permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY10013,USA),exceptforbriefexcerptsinconnectionwithreviewsorscholarlyanalysis.Usein connectionwithanyformofinformationstorageandretrieval,electronicadaptation,computersoftware, orbysimilarordissimilarmethodologynowknownorhereafterdevelopedisforbidden. Theuseinthispublicationoftradenames,trademarks,servicemarks,andsimilarterms,eveniftheyare notidentifiedassuch,isnottobetakenasanexpressionofopinionastowhetherornottheyaresubject toproprietaryrights. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Idedicatethisbooktomyparents, BarathandSona Preface Theideaforthisbookwasconceivedovermanyyearsandthroughmanyinfluences. The fields of neuropsychology, general neuroscience, and information technology were certainly among the main influences. It was in particular an unusual context inwhichIwasontheonehandexposedtoacademicandclinicalneuropsychology and on the other to information technology that gave rise to the ideas that would eventuallyleadtothiswork. Ibeganthinkingaboutinformaticsforneuropsychologymorethanadecadeago as a graduate student in behavioral neuroscience at Boston University School of Medicine.Mytrackinthisbroadinterdisciplinaryareacutacrossneuropsychology, neuroanatomyandneurobiology,andmyfocuswasvisualcognitiveneuroscience. I had concurrently held a position in a large information technology unit at the universitywhereIgainedexperienceincomputernetworksanddatabaseprogram- ming.Theneuropsychologycomponentofmytraininginvolvedneuropsychological assessment,whichwascarriedoutattheBostonVeteransAdministrationHospital, oneoftheteachinghospitalsofBostonUniversityMedicalSchool.Itwasatthese institutions that many legendary neuropsychologists had pioneered their craft and wheresomefamousassessmentinstrumentsweredeveloped. As I engaged in carrying out neuropsychological assessment, I could not help being struck by how comfortably this subspecialty of neuropsychology had con- tainedcriticalproblemstiedtoitsoriginsanditsdevelopment.Psychometrictesting hadplayedahugepartintheshapingofneuropsychologicalbatteriesandinsome cases assessment batteries were nothing more than modified psychometric tests. When tests were developed from scratch in clinical neuropsychology, they were typically developed around symptom clusters or operational tasks. Assessment tools bore little tie to highly defined neuroanatomic systems or to rich conceptual frameworks of cognition. Where was the alignment between neuropsychological assessment tools, which were developed in earlier generations, and that rich body of theory on neurocognitive principles that had arisen through cognitive neuro- science and cognitive neurobiology, in a more recent generation? The “decade of thebrain”hadbroughtforthsomanyneuralsystemsandmodulesthatrelated,with relativeprecision,cognitiveprocessestothebrain.Incomparison,neuropsycholog- ical assessment tools and neuropsychological models of cognition appeared rather unsophisticated. It would have been possible to strive for reconciliation between vii viii Preface assessment tools and functional neuroanatomic/neurocognitive systems if assess- ment took on a more computational dimension, but again, this consideration was absentinneuropsychology. My interest in the representational model of spatial neglect had me comb- ing through primate neuroscience literature on posterior parietal mechanisms for coordinate-based spatiotopic transformations. The conventional assessment tools for neglect, e.g., line bisection, letter cancellation, and clock and figure drawings, byvirtueoftheirsimplicity,couldgeneratedramaticpicturesofneglect,buthadno potentialtorelatetoneuralmodelsofneglect.Itwasthisproblemthatmademelook tocomputerizedmethods,whichinthiscasecouldbedevisedtotapintothecom- plexitiesofneglect.Ibeganworkonaninformaticssysteminvolvingagrid-based screen interfaced with a database. The coordinates of presented visual stimuli and thegradientsofneglectcouldberecordedandsubjectedtovariouskindsofanalysis (thisisdescribedinasubsectionofthisbook). Exploring informatics systems for neuropsychological applications inevitably hadmesurveyingthelargerfieldofbiologicalinformatics(bioinformatics)andits subspecialty in the neurosciences (neuroinformatics). The levels of sophistication attained by these disciplines were astounding as was the unique and transforma- tive potential that they conferred. It was evident that modern biomedical science was inseparable from bioinformatics. The Human Genome Project was in large part a bioinformatics project and so much of the Human Brain Project centered onneuroinformatics. The absence of neuropsychology on the vast and flourishing landscape of neuroinformatics was stark and striking. The scenario was that most of the sub- disciplines in neuroscience had discovered a powerful new technology, enabling novel methods of research, data analysis, problem solving, and knowledge build- ing. With neuroinformatics, they could capture, manipulate, and visualize data in waysneverbeforeconceived.Neuropsychology,however,remainedquiteoblivious to this informatics-based revolution in the neurosciences. Neuropsychology, espe- cially clinical neuropsychology, had by the 1980 s solidified an identity that had beenshapedovermanydecades.Ithaddevelopedamodusoperandithatwasinti- matelytiedtoitstoolsandmodels,mostofwhichwererootedinperiodsthatlong precededthemoderneraofcognitive-brainsciences.Bythelate1990s,informat- ics had become a tour de force in neuroscience, but neuropsychology, lying snug underitscanopyofconventions,showedalmostnoawarenessorunderstandingof thepotentialthatwasspelledbyneuroinformatics. In February 2005, I presented a paper at the US annual meeting of the Interna- tionalNeuropsychologicalSociety,inSt.Louis,Missouri.Thepaperdescribedthe impactofneuroinformaticsinneuroscience,andacasewaslaidoutforneuroinfor- maticsinneuropsychology.Isoonafterbegantostructurethepaperasamanuscript forareviewpublication.Researchforthepaperbroughtmeintocontactwithasmall butsteadilyincreasingnumberofindividualswhoseworkinneuropsychologytied in with informatics. They shared valuable data with me and were also keen about a larger account of neuroinformatics in neuropsychology. During this period, the Internet had also been transitioning from its first generation to its second, marked Preface ix by a host of web-based technologies for data modeling and collective knowledge building. Needless to say, with all these factors, what began as manuscript for a reviewpublicationquicklyevolvedintoabook. Thisbookintroducesthefieldofneuroinformaticstoneuropsychologists.Ittours the field of neuroinformatics and articulates ways by which neuroinformatics can be integrated with neuropsychological research and practice. It describes various applications for neuropsychology. The book is an ambitious first account of neu- roinformatics for neuropsychology – it discusses the kinds of changes required in thedisciplineforasuccessfulintegrationwithneuroinformatics,anditalsolaysout variousissuesthatarelikelytoariseasneuroinformaticsbecomesaneverydaypart of neuropsychology. It presents a vision of 21st century neuropsychology defined byneuroinformatics. The book is aimed at neuropsychologists and to those in related disciplines – behavioral neurology, psychiatry, clinical psychology, speech-language pathol- ogy,cognitivepsychology,andcognitiveneuroscience.Theintroductionofferedby this book is non-technical. The reader does not require a background in computer science or computational neuroscience. A reader of general neuropsychological literaturewillhavenoproblemunderstandingthematerialpresented. Numerous possibilities for the realization of neuroinformatics in neuropsy- chology are conveyed by this book. It is the author’s hope that the book will help accelerate discussion and enhance awareness of neuroinformatics for neu- ropsychology. A theme carried throughout the book is that neuroinformatics for neuropsychologyisnotanoptionbutaninevitabilitybroughtaboutbytechnological andtheoreticaladvancesofourtime. Boston,Massachusetts VinothJagaroo Acknowledgements Iamgratefultothemanyindividualswhohelpedmakethisbookpossible. TheencouragementandsupportIreceivedfrommycolleagues,DanielKempler, CynthiaBartlett,andDavidMaxwellintheDepartmentofCommunicationSciences andDisordersatEmersonCollege,wassimplyinvaluable.Theverysamemustbe saidofthemanyyearsofgeneroussupportthatIhavereceivedfromMarleneOscar BermanoftheBehavioralNeuroscienceProgramandtheDepartmentofAnatomy andNeurobiologyatBostonUniversitySchoolofMedicine. Research for a core section of the book, on neuroinformatics applications and models for neuropsychology, could not have been completed were it not for the cooperationthatIreceivedfromtwelveindividuals–whograciouslyaddressedmy inquiriesandprovidedmevaluabledataontheirwork:DennisReevesandJoseph Bleiberg(automatedneuropsychologicalassessment);MarkBaggett,MarkKelley, andDanielChristensen(Internet-enabledassessmentsystemspioneeredinclinical researchprogramsoftheUSArmy);Ho-ChuanHuang(computerizedcancellation testsystem);FrankGuenther(computationalmodelofspeechproduction);Huber- tusAxerandJanJantzen(aphasiadatabase);CarolNeidle(signlanguagedatabase project); Curtis Deutsch (behavioral phenomics and dysmorphology); and Robert Bilder(cognitiveandneuropsychiatricphenomics). I also wish to thank Stephen Koslow, the former director of the Office of Neu- roinformatics at the US National Institutes of Health, for reviewing my synthesis of the Human Brain Project, the Neuroinformatics Program of the National Insti- tutes of Health, and the Neuroinformatics Working Group of the Organization of EconomicCooperationandDevelopment. JaneEmes,mydiligentgraduatestudentassistantdeservesenormouscreditfor herassistancewithresearchandpreparationofthemanuscript. Finally, I am indebted to my colleague and friend, Jon Hemperley, the former managerofInformationTechnologyatOfficeofthePresidentatBostonUniversity, foryearsofmentorshiponinformationtechnologysystems. xi Contents 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 AnOverviewofBioinformatics . . . . . . . . . . . . . . . . . 1 1.2 WhatIsNeuroinformatics? . . . . . . . . . . . . . . . . . . . . 2 1.3 BringingNeuroinformaticstoNeuropsychology. . . . . . . . . 3 2 CurrentNeuroinformaticsApplicationsandInfrastructure . . . . 7 2.1 BrainImageConstruction,Analysis,andMorphometric Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.1.1 ExamplesofImageConstruction,Analysis, andMorphometricTools . . . . . . . . . . . . . . . . 8 2.2 BrainImageAtlases,DatabasesandRepositories . . . . . . . . 10 2.2.1 ExamplesofImageDatabases . . . . . . . . . . . . . 10 2.3 Toolsand Databases forMapping NeuralStructure andConnectivityPatterns . . . . . . . . . . . . . . . . . . . . 12 2.3.1 ExamplesofToolsandDatabasesfortheStudy ofNeuralArchitecture . . . . . . . . . . . . . . . . . 12 2.4 Tools and Methods for the Simulation of Neurons andNeuralCircuits . . . . . . . . . . . . . . . . . . . . . . . . 13 2.4.1 ExamplesofToolsfortheSimulationofNeurons . . . 14 2.5 Database and Knowledge Discovery Systems for ClinicalandAcademicResearch . . . . . . . . . . . . . . . . . 18 2.6 NeuroinformaticsManagementandInfrastructure . . . . . . . . 20 2.6.1 ExamplesofNIOrganizations,Infrastructure, andManagement . . . . . . . . . . . . . . . . . . . . 21 3 NeuroinformaticsforNeuropsychology . . . . . . . . . . . . . . . . 25 3.1 Differentiating Between the General Computer ApplicationsinNeuropsychologyandNeuroinformatics SystemsforNeuropsychology . . . . . . . . . . . . . . . . . . 25 3.2 DefiningNeuropsychology-SpecificNeuroinformatics Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 3.3 Neuroinformatics Applications and Models for Neuropsychology . . . . . . . . . . . . . . . . . . . . . . . . . 29 3.3.1 GeneralNeuropsychologicalAssessment . . . . . . . . 32 xiii
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