CalabCore
ThisrepositorycotaiscoretoolsforMRI/fMRI/PETaalysisfromtheCogitiveadAffectiveNeuorscieceLab(TorWager,PI)adourcollaborators.Mayofthesefuctiosareeededtoruothertoolboxes,e.g.,theCANlab’smultilevelmediatioadMartiLidquist’shemodyamicresposeestimatiotoolboxes.Abriefitroductiotothetoolboxcabefoudhere.
Thetoolsicludeobject-orietedtoolsfordoigeuroimagigaalysiswithsimplecommadsadscriptsthatprovidehigh-levelfuctioalityforeuroimagigaalysis.Forexample,thereisa"fmri_data"objecttypethatcotaiseuroimagigdatasets(bothPETadfMRIdataareok,despitetheame).Ifyouhavecreatedadobjectcalledmy_fmri_data_obj,theplot(my_fmri_data_obj)willgeerateaseriesofplotsspecifictoeuroimagigdata,icludigaiteractivebraiviewer(courtesyofSPMsoftware).predict(my_fmri_data_obj)willperformcross-validatedmultivariatepredictioofoutcomesbasedobraidata.ica(my_fmri_data_obj)willperformidepedetcompoetsaalysisothedata,adsoforth.
Therepositoryalsoicludesotherusefultoolboxes,icludig:
fMRIdesigoptimizatiousigageeticalgorithm(OptimizeGA)fMRIhemodyamicresposefuctioestimatio(HRF_Est_Toolbox2)fMRIaalysiswithHierarchicalExpoetiallyWeightedMovigAveragechage-poitaalysis(hewma_utility)VariousfMRIdiagostics(diagostics)MiscellaeousothertoolsadfuctiosforvisualizigbraidataGettighelpadadditioaliformatio:Wehaveseveralsourcesofdocumetatioforthistoolbox:
Forawalk-throughofacommobasicprocessigpipelie,seeourhackpadForfuctio-by-fuctiohelpdocumetsotheCoreToolsobjectsadfuctios,seethehelppagesoReadthedocs.Forbrief,documetedcodeexamplesofsomespecificfuctios,adabatchscriptsystemthatusestheCalabCoreobject-orietedtoolsforsecod-leveleuroimagigaalysis,seeCANlab_help_examplesgithubrepositoryTheCANlabwebsiteishttps://calabweb.colorado.edu/,adwealsomaitaiaWIKIwithmoreiformatioosomeofourtoolboxesadfMRIaalysismoregeerally,whichishere.FormoreiformatioofMRIaalysisgeerally,seeMartiadTor'soliebookadourfreeCourseravideosadclassesPriciplesoffMRIPart1adPart2.
Depedecies:TheseshouldbeistalledtousethistoolboxMatlabwww.mathworks.com
Matlabstatisticstoolbox
Matlabsigalprocessigtoolbox
StatisticalParametricMappig(SPM)softwarehttps://www.fil.io.ucl.ac.uk/spm/
matlab_bgl(graphtheory)adspider(machielearig)toolboxes;theseareicludedithisdistributio
theCANlabNeuroimagig_Patter_Masksrepositoryhttps://github.com/calab/Neuroimagig_Patter_Masks
thecalab_help_examplesrepositoryhttps://github.com/calab/CANlab_help_examples
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