RESTing-state fMRI data analysis toolkit (REST) Ma

RESTing-statefMRIdataanalysistoolkit(REST)ManualXiaoweiSong1,XiangyuLong1,YufengZang11StateKeyLaboratoryofCognitiveNeuroscienceandLearning,BeijingNormalUniversity,Beijing100875,China.May10,2008ThankXiangyuLongverymuchforthisEnglishmanual!--XiaoweiSongContentSomeabbreviations...........................................................................................................11.WhatcanyoudobyREST.............................................................................................12.NoticebeforeusingREST.............................................................................................23.StarttouseRESTtoolbox.............................................................................................33.1Installation..............................................................................................................33.2RemovetheREST....................................................................................................33.3StartREST...............................................................................................................33.4Regionalhomogeneityanalysis................................................................................43.4.1Whatisregionalhomogeneityanalysis...............................................................43.4.2.1Removelineartrend(optional)........................................................................63.4.2.2Temporalfilter(optional)................................................................................73.4.2.3Settingtheinputdata......................................................................................93.4.2.4Definethemaskoption.................................................................................103.4.2.5Definetheclustersize...................................................................................113.4.2.6Configuringtheoutputdirectory....................................................................113.4.2.7CalculatingtheReHomap............................................................................133.5ALFFanalysis.........................................................................................................153.5.1WhatistheALFFanalysis.................................................................................153.5.2.1SettingtheALFFparameters.........................................................................173.6Functionalconnectivityanalysis.............................................................................193.6.1Settingtheparametersoffunctionalconnectivityanalysis..............................204.Websites.....................................................................................................................305.Referencelist..............................................................................................................306.Acknowledgement......................................................................................................33REST1SomeabbreviationsAAL:AnatomicalAutomaticLabelingtemplate(Tzourio-Mazoyeretal.,2002)ALFF:amplitudeoflowfrequencyfluctuationAFNI:Freesoftware,website::functionalmagneticresonanceimagingGUI:GraphicalUserInterfaceMRIcron/Mricro:Freesoftware,website::regionalhomogeneityanalysisREST:RESTing-statefMRIdataanalysistoolkitROI:region-of-interestingSPM:Statisticalparametricmaps(Fristonetal.,1995),afreesoftware.1.WhatcanyoudobyREST1.BatchprocessingofthefMRIdataanalysis;2.PerformReHoanalysis,ALFFanalysisandlinearcorrelationanalysis;3.Band-passfilter,removelineartrendofthefMRIdata4.ViewingthetimeseriesandpowerspectrumofthefMRIdata5.DefinetheROI,extractthemeantimeserieswithintheROI;6.ViewingtheMRIimage,displaythefMRIresultonaanatomicalimage;REST27.ExtractthespecificclusterfromtheAALtemplate,Brodmanntemplateorstatisticmap,andcreatethemaskimage.2.NoticebeforeusingREST1.ImagefileformatmustbeANALYZE7.5,andMRIcronorAFNI(Cox,1996)canbeusedtotransformtheformat;2.WhenprocessingthefMRIdatabyREST,fMRIdataofeachsession(orsubject)mustbestoredinonefoldervolumebyvolume,i.e.,eachpairoffiles(hdr/img)isonetimepoint.Allvolumesmustbenamedintheorderofthescanningsequence,e.g.,thefMRIdataofonesubjectwasstoredintheindependentfolder,itmeansthattherewereexactlyallvolumesinthisfolderandthefilesinthisfoldermustlikethis:a001.hdr/img,a002.hdr/img,etc.Rememberthat,theunwantedimagefilemustbemovedoutofthefolder.3.WhenusingRESTtodefinetheseedvoxel,ifthecoordinatesofseedwasinputmanually,theoriginalandtheinputcoordinatesofallimagesmustbecorrected,andthepositionofROIcanbeviewedafterclickingthe“ViewROI”button.4.Citedthissoftwareas:RESTing-statefMRIdataanalysistoolkit(REST,bySongXiaowei,).REST33.StarttouseRESTtoolbox3.1Installationa)MATLAB2006bforWindowsXPwasrecommended.b)Unzipthepackage,thenstartMATLAB,choosetheoptionintoolbarasfollowing:File-SetPath...-AddFolder...(HereselecttheRESTfolder)-Save-Close.3.2Removeth