searchindex.js

Search.setIndex({objects:{"":{cocotools:[3,0,1,""]},"cocotools.MapGraph":{clean_data:[3,1,1,""],keep_only_one_level_of_resolution:[3,1,1,""],deduce_edges:[3,1,1,""]},cocotools:{query_maps_by_area:[3,2,1,""],EndGraph:[3,3,1,""],strip_absent_and_unknown_edges:[3,2,1,""],multi_map_ebunch:[3,2,1,""],ConGraph:[3,3,1,""],MapGraph:[3,3,1,""]},"cocotools.EndGraph":{add_translated_edges:[3,1,1,""]}},terms:{corpu:[5,7],suffici:[4,16],all:[1,2,5,6,7,3,10,15],code:[1,9,4,8,3,10,13],partial:[13,1],edg:[1,2,9,7,8,3,16,15],chain:[3,7],queri:[0,2,4,7,3,10,11],invent:4,four:13,concept:1,cocotools_area:2,follow:[1,2,4,7,3,10],primer:10,profici:4,congraph:[3,1,2,7,9],privat:[3,15],accur:[3,1],depend:7,graph:[0,1,2,9,3,4,7,10],flash:8,readabl:10,young:[13,10],send:9,articl:1,program:3,vec:8,n_nod:8,"case":[1,7],digit:13,sourc:[3,4,13,1,9],string:3,parcellarion:10,fals:3,multi_map_ebunch:[3,2],springer:1,unfamiliar:10,util:[0,4],ident:[13,3],worst:3,fall:13,veri:7,cocomac:[0,1,2,3,4,5,6,7,10,13],brows:2,differemt:10,level:[0,2,4,7,3,10,13],colleagu:[1,10],fewer:1,gut:1,quick:[13,6,10,7],per:[3,1],setup:12,pdc_hier:3,pleas:5,impli:[3,1,7],smaller:[13,3],natur:[10,16],seper:2,direct:[8,13,1,2,9],annot:13,past:2,consequ:1,second:[13,10],design:[3,4,1,10,6],pass:[10,3,2],download:[0,5,13,12],further:[13,2],click:[10,5,2],subclass:3,even:15,index:[3,0,6,8],what:[8,1,10,15],compar:1,brodmann:13,access:12,version:[3,10],"new":[3,8,1,10,7],net:[8,10],method:[0,1,2,5,7,3,10],deduc:[3,7,10],cull:10,full:[1,7],query_maps_by_area:[3,2],deriv:7,dropdown:2,mapgener:8,gener:[8,1],here:[0,1,2,3,5,6,7,10,12,13,15],modif:10,address:[13,1,2],path:[3,12],along:[13,10],modifi:[3,4,1],valu:[13,3],box:2,n_iter:8,search:[3,0,6,2],larger:[13,3,10],host:13,precis:[13,3],prior:1,implement:[3,1,10,7],transact:[13,7],although:13,curat:3,appli:[1,10,11,7],modul:[3,0,6,12,8],brainmap:3,mapping_non_timeout:2,releas:3,api:[3,6],uniqu:13,instal:[0,12],highli:12,plot:[4,10,11,14],from:[0,1,2,3,4,5,7,10,16,12,13],describ:[3,13,1,10],would:[3,10,7,2],liber:1,visit:12,two:[1,2,9,7,10,13],mort:[5,1,10,15],next:1,implic:3,few:4,call:[8,3,2],recommend:12,thru:[13,1,7],type:[3,1,2,12],until:[3,10],more:[1,2,3,10,13,15],sort:2,flaw:1,desir:2,endgraph:[1,9,5,3,16,15],hundr:7,relat:[1,9,7,3,10,13],notic:3,enhanc:3,warn:1,visual:13,floyd:7,connectivity_non_timeout:2,random_walk_steady_st:8,known:[3,2],hold:[3,1,2,9],cach:2,must:[3,13,1],none:3,retriev:13,hous:13,prepar:[1,10],work:[0,1,10],focu:15,cumbersom:2,conceptu:15,remain:3,can:[0,1,2,3,4,6,8,7,10,12],learn:[10,6,2,12],purpos:12,neuroinformat:13,control:4,claim:1,sqlite:2,pipelin:[4,6,10,11],stream:[6,10],give:10,process:[0,1,2,3,4,6,7,10,11,13,16],wank:7,registr:[1,9,7,3,10,11,15,16],share:[1,2],indic:[0,13,6],map_bunch_to:2,high:[0,10,4],want:[1,2,7,10,16,15],onlin:13,parcel:[10,1,2,9],alwai:[1,9],end:[3,7,10],mapg:[1,2,7],turn:4,rather:[1,10,16],anoth:1,write:10,how:[10,1,2,12],mapp:3,conn:3,reject:3,csv:5,simpl:[4,2],updat:[3,7],map:[1,2,9,7,8,3,10,13],overridden:3,huge:7,after:[3,10,7,2],neuroanatom:0,befor:2,notebook:[6,0,1,4],desired_map:3,klaa:10,mai:[13,7],multipl:10,redund:3,associ:3,grow:3,goal:7,principl:4,essenti:7,practic:1,pandya:13,preferr:2,correspond:3,exclud:3,issu:[1,7],inform:[3,8,1,16],maintain:4,combin:[3,10],allow:[3,4,1,7],mapequ:8,order:[13,10],origin:[3,13,1,16],help:[10,15],over:[4,13],failur:[13,3],becaus:3,brain:[0,2,7,9,10,13],paper:[0,5,1,10,13],through:[1,2,15],add_edg:3,hierarchi:[3,7],cortic:[1,10],paramet:2,macaqu:[0,13,10],mapfil:8,chosen:3,fix:7,better:8,window:12,complex:1,clu:8,main:[3,1],might:1,easier:2,them:[8,13,3,2],good:2,"return":[13,3,2,16],greater:3,thei:[4,7],python:[4,12],sentenc:3,overal:[6,10],dai:7,initi:[13,1],synopsi:10,module_end:8,now:2,discuss:[5,10],introduct:[13,6,10],term:3,neccessarili:1,name:[3,13,7],keep_only_one_level_of_resolut:[3,7],neccessari:4,revers:3,unlik:1,separ:1,truth:1,each:[1,2,9,7,3,13,15],fulli:[13,1],complet:[3,13,1],tracer:[13,1,2],search_typ:3,societi:[13,7],just:[3,7,10],weight:8,list:[3,7,2],individu:1,hard:[1,2],procedur:7,ensur:[3,7],"static":12,connect:[0,1,2,9,3,4,7,10,16,13],year:13,our:[1,10,7],ommis:7,event:3,special:2,out:[5,1,12],variabl:[7,2],accomplish:15,network:1,space:[1,7,9,16],miss:3,fv91:5,module_num:8,deduce_edg:[3,7],research:13,categori:13,suitabl:[4,13],explan:13,reader:13,ref:1,correct:3,matric:[0,5,4],pajek:8,mediat:3,insid:12,advanc:[13,10],ort:[1,5,7,3,10,15],manipul:2,situat:1,differ:[1,2,9,7,10,13],free:[1,9,4,7,3,10,11,12,15],standard:[4,7,2],small:1,base:[3,1,7],theori:[3,4,7,10],put:[1,2,7],pht00:[5,1,7],likelihood:3,basi:1,mapping_timeout:2,could:2,keep:[3,7,16],thing:[6,2],length:[8,3],enforc:3,place:[10,2],descript:[3,8,13,1,10],circuit:1,retain:7,subtl:1,imposs:7,first:[10,13,2,15],oper:4,softwar:4,major:10,finest:3,dont:2,directli:[10,3,2],onc:13,independ:[1,10,7],number:[3,7],rank:8,yourself:10,instruct:[0,12],unstudi:1,done:2,construct:3,open:12,primari:3,given:1,nomenclatur:3,unknown:[13,1,10,16],interact:[0,6,4],system:12,least:[1,10],stephan:[3,13,1,10,7],statement:[3,13,1,2],termin:[1,12],scheme:[10,13,1,2,9],"final":[1,10,16],store:[0,13,1],prone:[13,1],assign:[13,1],option:[4,3,2],relationship:[1,2,9,7,3,13],welcom:0,methodolog:[13,10],copi:[2,12],big_ebunch:3,specifi:[10,13,3,2],github:1,pars:[10,2],conserv:[1,10],than:[13,3,10],royal:[13,7],serv:7,target:[3,13,1,16,9],provid:[0,1,4,10,13,15],remov:[3,5,7,10,16],tree:8,biolog:[13,7],structur:[10,7,2],project:[4,3],applet:8,were:3,seri:[13,7],pre:[3,1,10,11,7],retrograd:[13,1],zill:[7,10],comput:[7,10,12],asbent:16,argument:4,raw:10,seed:8,have:[0,1,2,3,4,5,7,10],tabl:[0,6,2],disjoint:[3,7],seem:1,ambigu:7,strength:13,techniqu:7,zero:3,strip_absent_and_unknown_edg:[3,16],note:[3,8,1],mix:3,exampl:[0,1,2,4,6,7,16,13],take:[13,7,2],which:[2,4,8,3,10,12,13],tackl:10,tool:4,singl:[3,10,1,2,7],analysi:[4,13,10,11,14],cocotool:[0,1,2,3,4,6,7,9,10,16,12],distribut:12,preliminari:13,object:[1,2,9,6,7,3,10],clearer:10,aggeg:10,most:[1,2,4,7,3,10,16],pair:13,subset:[3,13,1,2],decomposit:8,clean_data:[3,7],"class":[3,1],don:8,gather:[10,7,2],cover:13,doe:[10,13,1,2],part:13,cortex:10,determin:[3,1],fact:[1,2],anterograd:[13,1],r00:[5,1],text:3,bring:1,session:12,networkx:[4,10,3,2,12],label:[1,16],data:[0,1,2,3,4,5,7,9,10,13],ground:1,xml:[10,13,2],current:[4,16],onli:[0,1,2,7,3,10,16,12,13],explicitli:7,locat:15,acquir:3,explain:7,solut:10,should:[3,10],brainsit:3,analyz:10,stain:[13,1,2,9],local:2,insight:7,variou:[3,4,1,7],get:[2,12],familiar:10,express:[13,9],autom:13,repo:12,cannot:3,report:13,requir:[10,13,7,2,12],enabl:3,borrow:[4,3,2],"public":[13,3],whether:[13,1,16],meanining:1,integr:[3,4,1,10],partit:8,contain:[8,13,1,2,9],kamper:[13,10],where:[10,9,2,12,6],valid:3,view:7,coarsest:3,set:[1,10,7],proce:1,knowledg:[13,2],see:[3,7],n_modul:8,mandatori:2,result:[1,2,9,3,4,8,7,10,11,13,16],fail:3,close:1,jocn:5,best:[3,1,7],subject:3,statu:10,wealth:0,mine:4,databas:[0,2,4,7,10,13],review:13,easi:[1,2],tend:10,state:[13,7],between:[1,2,7,8,3,13],"import":[13,1,10,7],approach:[1,10],across:[4,10],attribut:[3,9],altern:[10,2],assumpt:1,appreci:1,kei:10,amen:2,disallow:3,extens:[3,4,13,1,9],entir:[5,7,2],matplotlib:4,extent:[13,1,9],ipython:1,come:16,popul:2,both:[8,1,10,16],last:13,unstat:7,mistransl:1,region:[1,2,9,7,3,10,13],etc:4,mapgraph:[3,1,2,7,9],instanc:3,present:[3,1,10,16,9],logic:[10,1,2,7,6],let:15,pdc:[13,3],load:8,among:[3,7],simpli:10,endg:[1,16],technic:4,point:1,overview:[4,6,12],arbitrarili:3,header:10,featur:[10,1,2],littl:13,suppli:[3,4,13,1,10],module_id:8,assum:3,simpler:10,quit:10,ultim:7,why:10,numpi:4,due:3,been:[3,5,7,10],much:[4,10,1,2],ruleset:1,interest:[4,7],basic:10,unambigu:[1,7],futur:3,strategi:3,presenc:[13,1,2],thousand:7,resolut:[3,7],great:12,ani:[3,12],coordin:[1,9,7,3,10,11,15],understand:10,togeth:[1,7],demand:3,those:[3,10],sound:10,multi:2,therefor:2,look:1,affirm:1,ebunch:[3,2],aim:1,defin:1,"while":12,b05:[5,13],outcom:[7,10,16],abov:3,error:[3,1,16,7],coco:[1,2],aid:10,howev:[7,2,16,12],london:[13,7],subcort:5,advantag:1,readi:10,readm:12,non:[2,12],need:[1,2,4,7,10,12],cong:[3,1,2,7],crash:7,sever:[3,1,10,7],scienc:[13,7],develop:[13,3],clearli:1,author:13,perform:[1,2,9,4,7,3,10],make:[10,7,2,12],format:[8,10,3,2,13],same:[3,8,9,2,7],intra:3,overstep:1,handl:[3,1],html:8,largest:13,document:[0,6],anatom:[3,0,13,9,7],infer:[7,16],difficult:10,wheel:4,http:8,interrog:7,hand:1,infomap:8,depict:0,user:[0,2,4,7,3,10,16],mani:[13,7,10,16],desired_bmap:3,collat:[13,10],studi:[10,13,7,2],lower:2,kept:7,machineri:[9,7],neural:1,macro:[0,4],thu:[1,2,7],well:4,justifi:1,without:[3,7,10],command:[0,10,7,2,4],wherebi:2,thi:[1,2,7,8,3,10,12,13,15],choos:10,academ:12,propos:1,lest:7,comment:[3,7],openli:10,identifi:[3,7,15],entri:3,con_bunch:2,less:1,when:[1,2,7,3,16,13,15],laptop:7,converg:1,obtain:[1,10],human:10,speed:2,yet:[4,8],languag:2,begin:7,expos:10,also:[0,1,4,3,12,13],map_bunch:2,theoret:1,identif:3,add:[3,7,12],other:[3,8,7],input:[3,5,1,2,7],approxim:7,build:7,enthough:12,applic:3,around:4,transpar:1,read:8,add_edges_from:[3,2],know:[8,10,2],amp:[10,14],bit:2,bb47:5,formal:[1,10],like:16,specif:[13,7,10],relaion:1,resolv:7,integ:3,server:[10,13,3,2],collect:[0,13,4],petrid:13,either:1,output:[8,1,2,7],pp94:13,page:[0,6,12],targetmap:7,"function":[2,4,7,3,10,15],www:8,deduct:3,deal:2,captur:[13,1],some:[10,1,2],connectivity_timeout:2,certain:2,flow_map:8,kotter:[3,13,1,10,7],librari:[0,4],absent:[3,1,10,16],scale:[4,10],lead:[10,1,2],avoid:10,overlap:[3,13,7],mathemat:7,larg:[4,7,10],inject:[13,1],overcom:1,module_start:8,content:[0,6],notabl:10,overli:1,refer:[1,6,7,3,10,13,15],machin:10,core:1,encourag:13,sensibl:1,run:[1,2,8,7,10,15],timeout:2,slight:10,acronym:[13,1],burn:[13,10],step:[1,10,15,7,16],multitud:4,repositori:13,found:1,post:[3,10,11,16],handi:2,stage:10,chapter:1,about:[10,1,2,6],actual:10,interven:3,"_____":3,slightli:10,literatur:[3,4,7,10],unfortun:1,degre:3,produc:[4,1,2,7],routin:2,digraph:[3,2],regist:[0,1,7],within:[3,7],automat:3,three:[8,7],primat:13,empti:[3,1],strip:16,coodin:4,chang:3,connectom:4,your:[10,7,2,12],merg:3,websit:[13,2],span:13,wai:2,area:[13,7,2],transfer:3,support:13,transform:[3,4,1,10,7],"long":7,custom:[0,2],avail:[4,13,10,12],start:12,reli:1,interfac:3,includ:13,fraction:7,suit:[4,3],treat:1,fork:12,reorgan:13,form:[4,10,2,13,8],offer:[4,10],tupl:[3,2],back:16,link:8,translat:[1,7,3,10,16,15],line:[10,3,2],highest:3,"true":3,pull:3,made:[3,10],attr:3,consist:10,possibl:[3,13,1,10,7],"default":[3,4,7,2],displai:8,record:7,below:10,limit:13,absenc:[13,1,2],site:13,problem:[1,10,7],add_translated_edg:[3,1],agreg:[7,10],reciproc:9,creat:[0,2],classic:7,flow:[8,1],dure:[7,10],repres:[3,9,2,7],exist:[13,1],file:[8,3],n_edg:8,check:[5,1,2,12],assembl:1,mutual:7,excel:2,detail:[1,5,6,3,11,13,15],book:1,target_map:3,spatial:[1,9,7,3,10,13],test:13,tie:3,you:[1,2,6,7,10,12],node:[3,8,5,9,7],repeat:2,clean:[7,10],sequenc:3,org:[8,13],fewest:7,walker:13,consid:3,sql:[10,2],matrix:[7,10],reduc:7,philosoph:[13,7],receiv:9,faster:1,algorithm:[4,1,10,7],scientif:12,directori:[2,12],bozkurt:[13,10],berlin:1,ignor:[8,1],time:7,far:2},objtypes:{"0":"py:module","1":"py:method","2":"py:function","3":"py:class"},titles:["Welcome to CoCoTools!","Applying Coordinate-Free Registration","Querying","API reference","Overview","Data Downloads","CoCoTools’s documentation","Pre-Processing Query Results","Notes on running the Infomap Code","CoCoTools Objects","Overall Design Logic & Processing Stream","Processing Pipeline in Detail","Installation Instructions","Quick Introduction to CoCoMac","Plotting & Analysis","Coordinate-free registration in even more detail","Post-Processing"],objnames:{"0":["py","module","Python module"],"1":["py","method","Python method"],"2":["py","function","Python function"],"3":["py","class","Python class"]},filenames:["index","coordinatefreereg","querying","api","overview","downloads","documentation","preprocessing","infomap","objects","design","details","install","cocomac","plotting","endgraphguts","postprocessing"]})