ThisrepositorycontainscoretoolsforMRI/fMRI/PETanalysisfromtheCognitiveandAffectiveNeuorscienceLab(TorWager,PI)andourcollaborators.Manyofthesefunctionsareneededtorunothertoolboxes,e.g.,theCANlab’smultilevelmediationandMartinLindquist’shemodynamicresponseestimationtoolboxes.Abriefintroductiontothetoolboxcanbefoundhere.
Thetoolsincludeobject-orientedtoolsfordoingneuroimaginganalysiswithsimplecommandsandscriptsthatprovidehigh-levelfunctionalityforneuroimaginganalysis.Forexample,thereisan"fmri_data"objecttypethatcontainsneuroimagingdatasets(bothPETandfMRIdataareok,despitethename).Ifyouhavecreatedandobjectcalledmy_fmri_data_obj,thenplot(my_fmri_data_obj)willgenerateaseriesofplotsspecifictoneuroimagingdata,includinganinteractivebrainviewer(courtesyofSPMsoftware).predict(my_fmri_data_obj)willperformcross-validatedmultivariatepredictionofoutcomesbasedonbraindata.ica(my_fmri_data_obj)willperformindependentcomponentsanalysisonthedata,andsoforth.
Therepositoryalsoincludesotherusefultoolboxes,including:
fMRIdesignoptimizationusingageneticalgorithm(OptimizeGA)fMRIhemodynamicresponsefunctionestimation(HRF_Est_Toolbox2)fMRIanalysiswithHierarchicalExponentiallyWeightedMovingAveragechange-pointanalysis(hewma_utility)VariousfMRIdiagnostics(diagnostics)MiscellaneousothertoolsandfunctionsforvisualizingbraindataGettinghelpandadditionalinformation:Wehaveseveralsourcesofdocumentationforthistoolbox:
Forawalk-throughofacommonbasicprocessingpipeline,seeourhackpadForfunction-by-functionhelpdocumentsontheCoreToolsobjectsandfunctions,seethehelppagesonReadthedocs.Forbrief,documentedcodeexamplesofsomespecificfunctions,andabatchscriptsystemthatusestheCanlabCoreobject-orientedtoolsforsecond-levelneuroimaginganalysis,seeCANlab_help_examplesgithubrepositoryTheCANlabwebsiteishttps://canlabweb.colorado.edu/,andwealsomaintainaWIKIwithmoreinformationonsomeofourtoolboxesandfMRIanalysismoregenerally,whichishere.FormoreinformationonfMRIanalysisgenerally,seeMartinandTor'sonlinebookandourfreeCourseravideosandclassesPrinciplesoffMRIPart1andPart2.
Dependencies:TheseshouldbeinstalledtousethistoolboxMatlabwww.mathworks.com
Matlabstatisticstoolbox
Matlabsignalprocessingtoolbox
StatisticalParametricMapping(SPM)softwarehttps://www.fil.ion.ucl.ac.uk/spm/
matlab_bgl(graphtheory)andspider(machinelearning)toolboxes;theseareincludedinthisdistribution
theCANlabNeuroimaging_Pattern_Masksrepositoryhttps://github.com/canlab/Neuroimaging_Pattern_Masks
thecanlab_help_examplesrepositoryhttps://github.com/canlab/CANlab_help_examples
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