Unix Tutorial for FreeSurfer Users：UNIX教程Freesurfer用户.ppt

unixtutorialforfreesurferusers,enderkonukoglu,whatisunix/linux?,anoperatingsystem(likewindowsandosx)linuxisthefree,modifiable,andredistributableversionofunixwhyuseit?,whatisunix/linux?,anoperatingsystem(likewindowsandosx)linuxisthefree,modifiable,andredistributableversionofunixwhyuseit?powertowritemanyscriptswithmanycommandstoworkwithlotsofdatatousecomputerresourcesonthenetworkefficiently,suchasclusters,gettingstarted,communicatewithoperatingsystemthrougha“shell”orterminalwindow.forlinux:doubleclickterminaliconondesktopformacs:doubleclickonharddriveapplicationsutilitiesx11(doubleclick)applicationsutilitiesterminal,warmup,type:andhitenter.,date,warmup,type:andhitenter.shouldsee,date,monapr68:05:24edt2009,warmup,type:andhitenter.shouldseetype:andhitenter.,date,monapr68:05:24edt2009,cal,warmup,type:andhitenter.shouldseetype:andhitenter.shouldsee,date,monapr68:05:24edt2009,cal,april2009sumotuwethfrsa123456789101112131415161718192021222324252627282930,directories,unixusesahierarchicalfilesystem(thinkfoldersinwindows),directories,unixusesahierarchicalfilesystem(thinkfoldersinwindows),homeislike“mycomputer”,directories,unixusesahierarchicalfilesystem(thinkfoldersinwindows),homeislike“mycomputer”,like“mydocuments”,directories,unixusesahierarchicalfilesystem(thinkfoldersinwindows),homeislike“mycomputer”,like“mydocuments”,like“myphotos”,directories,unixusesahierarchicalfilesystem(thinkfoldersinwindows),homeislike“mycomputer”,like“mydocuments”,like“myphotos”,picture.jpg,location,type:andhitenter.shouldseeshows“presentworkingdirectory”orcurrentlocationasapathsimilarto:/mycomputer/mydocuments/myphotos,pwd,/home/nmrclass,/users/yourname,or,openingadirectory,notdoubleclickingtypecommandto“open”,commandstoopenfileswilldiffer,navigatingdirectories,“changedirectory”:moveintoafolder“list”:seecontentsofdirectory,ls,cd_,ls_,navigatingdirectories,“changedirectory”:moveintoafolder“list”:seecontentsofdirectory,ls,cd_,ls_,desktopmatlabtmptutorial_data,anatomyofacommand,command-option1option2file,command-help,anatomyofacommand,command-option1option2file,command-help,ls-help,try:,directorycontents,listcontentsofdirectoryyouareinlistsnamesofdirectories/files,ls,ls-lrt,ls-l,ls-a,directorycontents,listcontentsofdirectoryyouareinlistsnamesofdirectories/fileslistshiddenfilestoo,.xdebug_tkmedit.cshrc.alias,ls,ls-lrt,ls-l,ls-a,directorycontents,listcontentsofdirectoryyouareinlistsnamesofdirectories/fileslistshiddenfilestoolistsfiledetailsdrwxrwx-,user,group,others,ls,ls-lrt,ls-l,ls-a,directorycontents,listcontentsofdirectoryyouareinlistsnamesofdirectories/fileslistshiddenfilestoolistsfiledetailslistsrecentfileslast,ls,ls-lrt,ls-l,ls-a,savesometime,filenamecompletionhittabkeyshouldseehitenterhistoryhitkeyshouldseeshouldseetherecentcommands,lsdes,lsdesktop,lsdesktop,history,changingdirectories,makesanewdirectory“practice”changestodirectory“practice”,mkdirpractice,cdpractice,ls-lrt,pwd,ls,pwd,/home/nmrclass,/home/nmrclass/practice,shouldsee,shouldsee,shouldsee,nothing!,changingdirectories,changingdirectories,mkdirstuff,ls,makesfolder“stuff”insidepractice,shouldsee“stuff”,usinganeditor,ifusingamac:type:icouldwriteascriptinhere.filesave(buffer)fileexitemacsshouldsee“mynotes.txt”,emacsmynotes.txt,picomynotes.txt,ls,ctrl-xifusingpicoandthenyandenter,usinganeditor,ifusingamac:type:icouldwriteascriptinhere.filesave(buffer)fileexitemacsshouldsee“mynotes.txt”,geditmynotes.txt,picomynotes.txt,ls,ctrl-xifusingpicoandthenyandenter,usinganeditor,copyingfiles,ls,cp-help,cpmynotes.txtstuff,cdstuff,moremynotes.txt,learnalltheoptionsor“arguments”,isthecopycommand,cp,copyingfiles,ls,cp-help,cpmynotes.txtstuff,cdstuff,lessmynotes.txt,learnalltheoptionsor“arguments”,isthecopycommand,cp,changingdirectories,showsonedirectoryup,ls.,pwd,/home/nmrclass/practice/stuff,ls./.,goesuptwo!,cd.,shouldsee,cd./.,canalsodo(butdont):,copying/movingfiles,cpmynotes.txtmyothernotes.txt,couldalsousedo:,mvmyothernotes.txthernotes.txt,mvhernotes.txt.,removingfiles,rmmynotes.txt,ls,pwd,shouldbein“stuff”,ls,review,nodoubleclickingmkdirlscdpwdemacs,gedit,vi,picocprm,usingfreesurfer,withfreesurfer,certainvariablesmustbesetinordertouseitcorrectly:freesurfer_homesubjects_dir,telloperatingsystemwherefreesurferis,tellfreesurferwheredatais,requiredvariables,togotolocationofyourdata:$meanstakethevalueofthevariable,cd$subjects_dir,setenvsubjects_dir/path/to/data,requiredvariables,togotolocationofyourdata:$meanstakethevalueofthevariable,cd$subjects_dirakacd/path/to/data,setenvsubjects_dir/path/to/data,$,howechoworks:tosetavariable:tocheckwhatavariableissetto:,echo$test_variable,setenvtest_variableyourfirstname,echoitiscalledfootballnotsoccer.,requiredvariables,withfreesurfer,certainvariablesmustbesetinordertouseitcorrectly:freesurfer_homesubjects_dir,telloperatingsystemwherefreesurferis,tellfreesurferwheredatais,echo$freesurfer_home,echo$subjects_dir,tocheckvariables,visualizationtools,forfreesurfervisualizationtools:,tkmeditsubj001t1.mgz-auxwm.mgz,tksurfersubj001lhinflated,visualizationtoolsubjectdata_file-auxother_data_file,visualizationtoolsubjecthemispheredata_file,freeviewvolume1volume2-fsurface1surface2,morehelp,/fswiki/fstutorial/commandlinenavigationlinksonwikiunder“unixtutorial”glossaryofunixcommands,theend,goodluck!,writingscripts,puttingmultiplecommandstogether.automaticallyrunningasequenceofcommandsexample:createafilenamedmy_first_script.cshwiththecontents:,#!/bin/cshsetenvnamefreesurferechoilove$name!,%chmodu+xmy_first_script.csh%./my_first_script.csh,loopsinscripts,youcancreateloops,ifstatements,example:createafilenamedmy_fir