| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696697698699700701702703704705706707708709710711712713714715716717718719720721722723724725726727728729730731732733734735736737738739740741742743744745746747748749750751752753754755756757758759760761762763764765766767768769770771772773774775776777778779780781782783784785786787788789790791792793794795796797798799800801802803804805806807808809810811812813814815816817818819820821822823824825826827828829830831832833834835836837838839840841842843844845846847848849850851852853854855856857858859860861862863864865866867868869870871872873874875876877878879880881882883884885886887888889890891892893894895896897898899900901902903904905906907908909910911912913914915916917918919920921922923924925926927928929930931932933934935936937938939940941942943944945946947948949950951952953954955956957958959960961962963964965966967968969970971972973974975976977978979980981982983984985986987988989990991992993994995996997998999100010011002100310041005100610071008100910101011101210131014101510161017101810191020102110221023102410251026102710281029103010311032103310341035103610371038103910401041104210431044104510461047104810491050105110521053105410551056105710581059106010611062106310641065106610671068106910701071107210731074107510761077107810791080108110821083108410851086108710881089109010911092109310941095109610971098109911001101110211031104110511061107110811091110111111121113111411151116111711181119112011211122112311241125112611271128112911301131113211331134113511361137113811391140114111421143114411451146114711481149115011511152115311541155115611571158115911601161116211631164116511661167116811691170117111721173117411751176117711781179118011811182118311841185118611871188118911901191119211931194119511961197119811991200120112021203120412051206120712081209121012111212121312141215121612171218121912201221122212231224122512261227122812291230123112321233123412351236123712381239124012411242124312441245124612471248124912501251125212531254125512561257125812591260126112621263126412651266126712681269127012711272127312741275127612771278127912801281128212831284128512861287128812891290129112921293129412951296129712981299130013011302130313041305130613071308130913101311131213131314131513161317131813191320132113221323132413251326132713281329133013311332133313341335133613371338133913401341134213431344134513461347134813491350135113521353135413551356135713581359136013611362136313641365136613671368136913701371137213731374137513761377137813791380138113821383138413851386138713881389139013911392139313941395139613971398139914001401140214031404140514061407140814091410141114121413141414151416141714181419142014211422142314241425142614271428142914301431143214331434143514361437143814391440144114421443144414451446144714481449145014511452145314541455145614571458145914601461146214631464146514661467146814691470147114721473147414751476147714781479148014811482148314841485148614871488148914901491149214931494149514961497149814991500150115021503150415051506150715081509151015111512151315141515151615171518151915201521152215231524152515261527152815291530153115321533153415351536153715381539154015411542154315441545154615471548154915501551155215531554155515561557155815591560156115621563156415651566156715681569157015711572157315741575157615771578157915801581158215831584158515861587158815891590159115921593159415951596159715981599160016011602160316041605160616071608160916101611161216131614161516161617161816191620162116221623162416251626162716281629163016311632163316341635163616371638163916401641164216431644164516461647164816491650165116521653165416551656165716581659166016611662166316641665166616671668166916701671167216731674167516761677167816791680168116821683168416851686168716881689169016911692169316941695169616971698169917001701170217031704170517061707170817091710171117121713171417151716171717181719172017211722172317241725172617271728172917301731173217331734173517361737173817391740174117421743174417451746174717481749175017511752175317541755175617571758175917601761176217631764176517661767176817691770177117721773177417751776177717781779178017811782178317841785178617871788178917901791179217931794179517961797179817991800180118021803180418051806180718081809181018111812181318141815181618171818181918201821182218231824182518261827182818291830183118321833183418351836183718381839184018411842184318441845184618471848184918501851185218531854185518561857185818591860186118621863186418651866186718681869187018711872187318741875187618771878187918801881188218831884188518861887188818891890189118921893189418951896189718981899190019011902190319041905190619071908190919101911191219131914191519161917191819191920192119221923192419251926192719281929193019311932193319341935193619371938193919401941194219431944194519461947194819491950195119521953195419551956195719581959196019611962196319641965196619671968196919701971197219731974197519761977197819791980198119821983198419851986198719881989199019911992199319941995199619971998199920002001200220032004200520062007200820092010201120122013201420152016201720182019202020212022202320242025202620272028202920302031203220332034203520362037203820392040204120422043204420452046204720482049205020512052205320542055205620572058205920602061206220632064206520662067206820692070207120722073207420752076207720782079208020812082208320842085208620872088208920902091209220932094209520962097209820992100210121022103210421052106210721082109211021112112211321142115211621172118211921202121212221232124212521262127212821292130213121322133213421352136213721382139214021412142214321442145214621472148214921502151215221532154215521562157215821592160216121622163216421652166216721682169217021712172217321742175217621772178217921802181218221832184218521862187218821892190219121922193219421952196219721982199220022012202220322042205220622072208220922102211221222132214221522162217221822192220222122222223222422252226222722282229223022312232223322342235223622372238223922402241224222432244224522462247224822492250225122522253225422552256225722582259226022612262226322642265226622672268226922702271227222732274227522762277227822792280228122822283228422852286228722882289229022912292229322942295229622972298229923002301230223032304230523062307230823092310231123122313231423152316231723182319232023212322232323242325232623272328232923302331233223332334233523362337233823392340234123422343234423452346234723482349235023512352235323542355235623572358235923602361236223632364236523662367236823692370237123722373237423752376237723782379238023812382238323842385238623872388238923902391239223932394239523962397239823992400240124022403240424052406240724082409241024112412241324142415241624172418241924202421242224232424242524262427242824292430243124322433243424352436243724382439244024412442244324442445244624472448244924502451245224532454245524562457245824592460246124622463246424652466246724682469247024712472247324742475247624772478247924802481248224832484248524862487248824892490249124922493249424952496249724982499250025012502250325042505250625072508250925102511251225132514251525162517251825192520252125222523252425252526252725282529253025312532253325342535253625372538253925402541254225432544254525462547254825492550255125522553255425552556255725582559256025612562256325642565256625672568256925702571257225732574257525762577257825792580258125822583258425852586258725882589259025912592259325942595259625972598259926002601260226032604260526062607260826092610261126122613261426152616261726182619262026212622262326242625262626272628262926302631263226332634263526362637263826392640264126422643264426452646264726482649265026512652265326542655265626572658265926602661266226632664266526662667266826692670267126722673267426752676267726782679268026812682268326842685268626872688268926902691269226932694269526962697269826992700270127022703270427052706270727082709271027112712271327142715271627172718271927202721272227232724272527262727272827292730273127322733273427352736273727382739274027412742274327442745274627472748274927502751275227532754275527562757275827592760276127622763276427652766276727682769277027712772277327742775277627772778277927802781278227832784278527862787278827892790279127922793279427952796279727982799280028012802280328042805280628072808280928102811281228132814281528162817281828192820282128222823282428252826282728282829283028312832283328342835283628372838283928402841284228432844284528462847284828492850285128522853285428552856285728582859286028612862286328642865286628672868286928702871287228732874287528762877287828792880288128822883288428852886288728882889289028912892289328942895289628972898289929002901290229032904290529062907290829092910291129122913291429152916291729182919292029212922292329242925292629272928292929302931293229332934293529362937293829392940294129422943294429452946294729482949295029512952295329542955295629572958295929602961296229632964296529662967296829692970297129722973297429752976297729782979298029812982298329842985298629872988298929902991299229932994299529962997299829993000300130023003300430053006300730083009301030113012301330143015301630173018301930203021302230233024302530263027302830293030303130323033303430353036303730383039304030413042304330443045304630473048304930503051305230533054305530563057305830593060306130623063306430653066306730683069307030713072307330743075307630773078307930803081308230833084308530863087308830893090309130923093309430953096309730983099310031013102310331043105310631073108310931103111311231133114311531163117311831193120312131223123312431253126312731283129313031313132313331343135313631373138313931403141314231433144314531463147314831493150315131523153315431553156315731583159316031613162316331643165316631673168316931703171317231733174317531763177317831793180318131823183318431853186318731883189319031913192319331943195319631973198319932003201320232033204320532063207320832093210321132123213321432153216321732183219322032213222322332243225322632273228322932303231323232333234323532363237323832393240324132423243324432453246324732483249325032513252325332543255325632573258325932603261326232633264326532663267326832693270327132723273327432753276327732783279328032813282328332843285328632873288328932903291329232933294329532963297329832993300330133023303330433053306330733083309331033113312331333143315331633173318331933203321332233233324332533263327332833293330333133323333333433353336333733383339334033413342334333443345334633473348334933503351335233533354335533563357335833593360336133623363336433653366336733683369337033713372337333743375337633773378337933803381338233833384338533863387338833893390339133923393339433953396339733983399340034013402340334043405340634073408340934103411341234133414341534163417341834193420342134223423342434253426342734283429343034313432343334343435343634373438343934403441344234433444344534463447344834493450345134523453345434553456345734583459346034613462346334643465346634673468346934703471347234733474347534763477347834793480348134823483348434853486348734883489349034913492349334943495349634973498349935003501350235033504350535063507350835093510351135123513351435153516351735183519352035213522352335243525352635273528352935303531353235333534353535363537353835393540354135423543354435453546354735483549355035513552355335543555355635573558355935603561356235633564356535663567356835693570357135723573357435753576357735783579358035813582358335843585358635873588358935903591359235933594359535963597359835993600360136023603360436053606360736083609361036113612361336143615361636173618361936203621362236233624362536263627362836293630363136323633363436353636363736383639364036413642364336443645364636473648364936503651365236533654365536563657365836593660366136623663366436653666366736683669367036713672367336743675367636773678367936803681368236833684368536863687368836893690369136923693369436953696369736983699370037013702370337043705370637073708370937103711371237133714371537163717371837193720372137223723372437253726372737283729373037313732373337343735373637373738373937403741374237433744374537463747374837493750375137523753375437553756375737583759376037613762376337643765376637673768376937703771377237733774377537763777377837793780378137823783378437853786378737883789379037913792379337943795379637973798379938003801380238033804380538063807380838093810381138123813381438153816381738183819382038213822382338243825382638273828382938303831383238333834383538363837383838393840384138423843384438453846384738483849385038513852385338543855385638573858385938603861386238633864386538663867386838693870387138723873387438753876387738783879388038813882388338843885388638873888388938903891389238933894389538963897389838993900390139023903390439053906390739083909391039113912391339143915391639173918391939203921392239233924392539263927392839293930393139323933393439353936393739383939394039413942394339443945394639473948394939503951395239533954395539563957395839593960396139623963396439653966396739683969397039713972397339743975397639773978397939803981398239833984398539863987398839893990399139923993399439953996399739983999400040014002400340044005400640074008400940104011401240134014401540164017401840194020402140224023402440254026402740284029403040314032403340344035403640374038403940404041404240434044404540464047404840494050405140524053405440554056405740584059406040614062406340644065406640674068406940704071407240734074407540764077407840794080408140824083408440854086408740884089409040914092409340944095409640974098409941004101410241034104410541064107410841094110411141124113411441154116411741184119412041214122412341244125412641274128412941304131413241334134413541364137413841394140414141424143414441454146414741484149415041514152415341544155415641574158415941604161416241634164416541664167416841694170417141724173417441754176417741784179418041814182418341844185418641874188418941904191419241934194419541964197419841994200420142024203420442054206420742084209421042114212421342144215421642174218421942204221422242234224422542264227422842294230423142324233423442354236423742384239424042414242424342444245424642474248424942504251425242534254425542564257425842594260426142624263426442654266426742684269427042714272427342744275427642774278427942804281428242834284428542864287428842894290429142924293429442954296429742984299430043014302430343044305430643074308430943104311431243134314431543164317431843194320432143224323432443254326432743284329433043314332433343344335433643374338433943404341434243434344434543464347434843494350435143524353435443554356435743584359436043614362436343644365436643674368436943704371437243734374437543764377437843794380438143824383438443854386438743884389439043914392439343944395439643974398439944004401440244034404440544064407440844094410441144124413441444154416441744184419442044214422442344244425442644274428442944304431443244334434443544364437443844394440444144424443444444454446444744484449445044514452445344544455445644574458445944604461446244634464446544664467446844694470447144724473447444754476447744784479448044814482448344844485448644874488448944904491449244934494449544964497449844994500450145024503450445054506450745084509451045114512451345144515451645174518451945204521452245234524452545264527452845294530453145324533453445354536453745384539454045414542454345444545454645474548454945504551455245534554455545564557455845594560456145624563456445654566456745684569457045714572457345744575457645774578457945804581458245834584458545864587458845894590459145924593459445954596459745984599460046014602460346044605460646074608460946104611461246134614461546164617461846194620462146224623462446254626462746284629463046314632463346344635463646374638463946404641464246434644464546464647464846494650465146524653465446554656465746584659466046614662466346644665466646674668466946704671467246734674467546764677467846794680468146824683468446854686468746884689469046914692469346944695469646974698469947004701470247034704470547064707470847094710471147124713471447154716471747184719472047214722472347244725472647274728472947304731473247334734473547364737473847394740474147424743474447454746474747484749475047514752475347544755475647574758475947604761476247634764476547664767476847694770477147724773477447754776477747784779478047814782478347844785478647874788478947904791479247934794479547964797479847994800480148024803480448054806480748084809481048114812481348144815481648174818481948204821482248234824482548264827482848294830483148324833483448354836483748384839484048414842484348444845484648474848484948504851485248534854485548564857485848594860486148624863486448654866486748684869487048714872487348744875487648774878487948804881488248834884488548864887488848894890489148924893489448954896489748984899490049014902490349044905490649074908490949104911491249134914491549164917491849194920492149224923492449254926492749284929493049314932493349344935493649374938493949404941494249434944494549464947494849494950495149524953495449554956495749584959496049614962496349644965496649674968496949704971497249734974497549764977497849794980498149824983498449854986498749884989499049914992499349944995499649974998499950005001500250035004500550065007500850095010501150125013501450155016501750185019502050215022502350245025502650275028502950305031503250335034503550365037503850395040504150425043504450455046504750485049505050515052505350545055505650575058505950605061506250635064506550665067506850695070507150725073507450755076507750785079508050815082508350845085508650875088508950905091509250935094509550965097509850995100510151025103510451055106510751085109511051115112511351145115511651175118511951205121512251235124512551265127512851295130513151325133513451355136513751385139514051415142514351445145514651475148514951505151515251535154515551565157515851595160516151625163516451655166516751685169517051715172517351745175517651775178517951805181518251835184518551865187518851895190519151925193519451955196519751985199520052015202520352045205520652075208520952105211521252135214521552165217521852195220522152225223522452255226522752285229523052315232523352345235523652375238523952405241524252435244524552465247524852495250525152525253525452555256525752585259526052615262526352645265526652675268526952705271527252735274527552765277527852795280528152825283528452855286528752885289529052915292529352945295529652975298529953005301530253035304530553065307530853095310531153125313531453155316531753185319532053215322532353245325532653275328532953305331533253335334533553365337533853395340534153425343534453455346534753485349535053515352535353545355535653575358535953605361536253635364536553665367536853695370537153725373537453755376537753785379538053815382538353845385538653875388538953905391539253935394539553965397539853995400540154025403540454055406540754085409541054115412541354145415541654175418541954205421542254235424542554265427542854295430543154325433543454355436543754385439544054415442544354445445544654475448544954505451545254535454545554565457545854595460546154625463546454655466546754685469547054715472547354745475547654775478547954805481548254835484548554865487548854895490549154925493549454955496549754985499550055015502550355045505550655075508550955105511551255135514551555165517551855195520552155225523552455255526552755285529553055315532553355345535553655375538553955405541554255435544554555465547554855495550555155525553555455555556555755585559556055615562556355645565556655675568556955705571557255735574557555765577557855795580558155825583558455855586558755885589559055915592559355945595559655975598559956005601560256035604560556065607560856095610561156125613561456155616561756185619562056215622562356245625562656275628562956305631563256335634563556365637563856395640564156425643564456455646564756485649565056515652565356545655565656575658565956605661566256635664566556665667566856695670567156725673567456755676567756785679568056815682568356845685568656875688568956905691569256935694569556965697569856995700570157025703570457055706570757085709571057115712571357145715571657175718571957205721572257235724572557265727572857295730573157325733573457355736573757385739574057415742574357445745574657475748574957505751575257535754575557565757575857595760576157625763576457655766576757685769577057715772577357745775577657775778577957805781578257835784578557865787578857895790579157925793579457955796579757985799580058015802580358045805580658075808580958105811581258135814581558165817581858195820582158225823582458255826582758285829583058315832583358345835583658375838583958405841584258435844584558465847584858495850585158525853585458555856585758585859586058615862586358645865586658675868586958705871587258735874587558765877587858795880588158825883588458855886588758885889589058915892589358945895589658975898589959005901590259035904590559065907590859095910591159125913591459155916591759185919592059215922592359245925592659275928592959305931593259335934593559365937593859395940594159425943594459455946594759485949595059515952595359545955595659575958595959605961596259635964596559665967596859695970597159725973597459755976597759785979598059815982598359845985598659875988598959905991599259935994599559965997599859996000600160026003600460056006600760086009601060116012601360146015601660176018601960206021602260236024602560266027602860296030603160326033603460356036603760386039604060416042604360446045604660476048604960506051605260536054605560566057605860596060606160626063606460656066606760686069607060716072607360746075607660776078607960806081608260836084608560866087608860896090609160926093609460956096609760986099610061016102610361046105610661076108610961106111611261136114611561166117611861196120612161226123612461256126612761286129613061316132613361346135613661376138613961406141614261436144614561466147614861496150615161526153615461556156615761586159616061616162616361646165616661676168616961706171617261736174617561766177617861796180618161826183618461856186618761886189619061916192619361946195619661976198619962006201620262036204620562066207620862096210621162126213621462156216621762186219622062216222622362246225622662276228622962306231623262336234623562366237623862396240624162426243624462456246624762486249625062516252625362546255625662576258625962606261626262636264626562666267626862696270627162726273627462756276627762786279628062816282628362846285628662876288628962906291629262936294629562966297629862996300630163026303630463056306630763086309631063116312631363146315631663176318631963206321632263236324632563266327632863296330633163326333633463356336633763386339634063416342634363446345634663476348634963506351635263536354635563566357635863596360636163626363636463656366636763686369637063716372637363746375637663776378637963806381638263836384638563866387638863896390639163926393639463956396639763986399640064016402640364046405640664076408640964106411641264136414641564166417641864196420642164226423642464256426642764286429643064316432643364346435643664376438643964406441644264436444644564466447644864496450645164526453645464556456645764586459646064616462646364646465646664676468646964706471647264736474647564766477647864796480648164826483648464856486648764886489649064916492649364946495649664976498649965006501650265036504650565066507650865096510651165126513651465156516651765186519652065216522652365246525652665276528652965306531653265336534653565366537653865396540654165426543654465456546654765486549655065516552655365546555655665576558655965606561656265636564656565666567656865696570657165726573657465756576657765786579658065816582658365846585658665876588658965906591659265936594659565966597659865996600660166026603660466056606660766086609661066116612661366146615661666176618661966206621662266236624662566266627662866296630663166326633663466356636663766386639664066416642664366446645664666476648664966506651665266536654665566566657665866596660666166626663666466656666666766686669667066716672667366746675667666776678667966806681668266836684668566866687668866896690669166926693669466956696669766986699670067016702670367046705670667076708670967106711671267136714671567166717671867196720672167226723672467256726672767286729673067316732673367346735673667376738673967406741674267436744674567466747674867496750675167526753675467556756675767586759676067616762676367646765676667676768676967706771677267736774677567766777677867796780678167826783678467856786678767886789679067916792679367946795679667976798679968006801680268036804680568066807680868096810681168126813681468156816681768186819682068216822682368246825682668276828682968306831683268336834683568366837683868396840684168426843684468456846684768486849685068516852685368546855685668576858685968606861686268636864686568666867686868696870687168726873687468756876687768786879688068816882688368846885688668876888688968906891689268936894689568966897689868996900690169026903690469056906690769086909691069116912691369146915691669176918691969206921692269236924692569266927692869296930693169326933693469356936693769386939694069416942694369446945694669476948694969506951695269536954695569566957695869596960696169626963696469656966696769686969697069716972697369746975697669776978697969806981698269836984698569866987698869896990699169926993699469956996699769986999700070017002700370047005700670077008700970107011701270137014701570167017701870197020702170227023702470257026702770287029703070317032703370347035703670377038703970407041704270437044704570467047704870497050705170527053705470557056705770587059706070617062706370647065706670677068706970707071707270737074707570767077707870797080708170827083708470857086708770887089709070917092709370947095709670977098709971007101710271037104710571067107710871097110711171127113711471157116711771187119712071217122712371247125712671277128712971307131713271337134713571367137713871397140714171427143714471457146714771487149715071517152715371547155715671577158715971607161716271637164716571667167716871697170717171727173717471757176717771787179718071817182718371847185718671877188718971907191719271937194719571967197719871997200720172027203720472057206720772087209721072117212721372147215721672177218721972207221722272237224722572267227722872297230723172327233723472357236723772387239724072417242724372447245724672477248724972507251725272537254725572567257725872597260726172627263726472657266726772687269727072717272727372747275727672777278727972807281728272837284728572867287728872897290729172927293729472957296729772987299730073017302730373047305730673077308730973107311731273137314731573167317731873197320732173227323732473257326732773287329733073317332733373347335733673377338733973407341734273437344734573467347734873497350735173527353735473557356735773587359736073617362736373647365736673677368736973707371737273737374737573767377737873797380738173827383738473857386738773887389739073917392739373947395739673977398739974007401740274037404740574067407740874097410741174127413741474157416741774187419742074217422742374247425742674277428742974307431743274337434743574367437743874397440744174427443744474457446744774487449745074517452745374547455745674577458745974607461746274637464746574667467746874697470747174727473747474757476747774787479748074817482748374847485748674877488748974907491749274937494749574967497749874997500750175027503750475057506750775087509751075117512751375147515751675177518751975207521752275237524752575267527752875297530753175327533753475357536753775387539754075417542754375447545754675477548754975507551755275537554755575567557755875597560756175627563756475657566756775687569757075717572757375747575757675777578757975807581758275837584758575867587758875897590759175927593759475957596759775987599760076017602760376047605760676077608760976107611761276137614761576167617761876197620762176227623762476257626762776287629763076317632763376347635763676377638763976407641764276437644764576467647764876497650765176527653765476557656765776587659766076617662766376647665766676677668766976707671767276737674767576767677767876797680768176827683768476857686768776887689769076917692769376947695769676977698769977007701770277037704770577067707770877097710771177127713771477157716771777187719772077217722772377247725772677277728772977307731773277337734773577367737773877397740774177427743774477457746774777487749775077517752775377547755775677577758775977607761776277637764776577667767776877697770777177727773777477757776777777787779778077817782778377847785778677877788778977907791779277937794779577967797779877997800780178027803780478057806780778087809781078117812781378147815781678177818781978207821782278237824782578267827782878297830783178327833783478357836783778387839784078417842784378447845784678477848784978507851785278537854785578567857785878597860786178627863786478657866786778687869787078717872787378747875787678777878787978807881788278837884788578867887788878897890789178927893789478957896789778987899790079017902790379047905790679077908790979107911791279137914791579167917791879197920792179227923792479257926792779287929793079317932793379347935793679377938793979407941794279437944794579467947794879497950795179527953795479557956795779587959796079617962796379647965796679677968796979707971797279737974797579767977797879797980798179827983798479857986798779887989799079917992799379947995799679977998799980008001800280038004800580068007800880098010801180128013801480158016801780188019802080218022802380248025802680278028802980308031803280338034803580368037803880398040804180428043804480458046804780488049805080518052805380548055805680578058805980608061806280638064806580668067806880698070807180728073807480758076807780788079808080818082808380848085808680878088808980908091809280938094809580968097809880998100810181028103810481058106810781088109811081118112811381148115811681178118811981208121812281238124812581268127812881298130813181328133813481358136813781388139814081418142814381448145814681478148814981508151815281538154815581568157815881598160816181628163816481658166816781688169817081718172817381748175817681778178817981808181818281838184818581868187818881898190819181928193819481958196819781988199820082018202820382048205820682078208820982108211821282138214821582168217821882198220822182228223822482258226822782288229823082318232823382348235823682378238823982408241824282438244824582468247824882498250825182528253825482558256825782588259826082618262826382648265826682678268826982708271827282738274827582768277827882798280828182828283828482858286828782888289829082918292829382948295829682978298829983008301830283038304830583068307830883098310831183128313831483158316831783188319832083218322832383248325832683278328832983308331833283338334833583368337833883398340834183428343834483458346834783488349835083518352835383548355835683578358835983608361836283638364836583668367836883698370837183728373837483758376837783788379838083818382838383848385838683878388838983908391839283938394839583968397839883998400840184028403840484058406840784088409841084118412841384148415841684178418841984208421842284238424842584268427842884298430843184328433843484358436843784388439844084418442844384448445844684478448844984508451845284538454845584568457845884598460846184628463846484658466846784688469847084718472847384748475847684778478847984808481848284838484848584868487848884898490849184928493849484958496849784988499850085018502850385048505850685078508850985108511851285138514851585168517851885198520852185228523852485258526852785288529853085318532853385348535853685378538853985408541854285438544854585468547854885498550855185528553855485558556855785588559856085618562856385648565856685678568856985708571857285738574857585768577857885798580858185828583858485858586858785888589859085918592859385948595859685978598859986008601860286038604860586068607860886098610861186128613861486158616861786188619862086218622862386248625862686278628862986308631863286338634863586368637863886398640864186428643864486458646864786488649865086518652865386548655865686578658865986608661866286638664866586668667866886698670867186728673867486758676867786788679868086818682868386848685868686878688868986908691869286938694869586968697869886998700870187028703870487058706870787088709871087118712871387148715871687178718871987208721872287238724872587268727872887298730873187328733873487358736873787388739874087418742874387448745874687478748874987508751875287538754875587568757875887598760876187628763876487658766876787688769877087718772877387748775877687778778877987808781878287838784878587868787878887898790879187928793879487958796879787988799880088018802880388048805880688078808880988108811881288138814881588168817881888198820882188228823882488258826882788288829883088318832883388348835883688378838883988408841884288438844884588468847884888498850885188528853885488558856885788588859886088618862886388648865886688678868886988708871887288738874887588768877887888798880888188828883888488858886888788888889889088918892889388948895889688978898889989008901890289038904890589068907890889098910891189128913891489158916891789188919892089218922892389248925892689278928892989308931893289338934893589368937893889398940894189428943894489458946894789488949895089518952895389548955895689578958895989608961896289638964896589668967896889698970897189728973897489758976897789788979898089818982898389848985898689878988898989908991899289938994899589968997899889999000900190029003900490059006900790089009901090119012901390149015901690179018901990209021902290239024902590269027902890299030903190329033903490359036903790389039904090419042904390449045904690479048904990509051905290539054905590569057905890599060906190629063906490659066906790689069907090719072907390749075907690779078907990809081908290839084908590869087908890899090909190929093909490959096909790989099910091019102910391049105910691079108910991109111911291139114911591169117911891199120912191229123912491259126912791289129913091319132913391349135913691379138913991409141914291439144914591469147914891499150915191529153915491559156915791589159916091619162916391649165916691679168916991709171917291739174917591769177917891799180918191829183918491859186918791889189919091919192919391949195919691979198919992009201920292039204920592069207920892099210921192129213921492159216921792189219922092219222922392249225922692279228922992309231923292339234923592369237923892399240924192429243924492459246924792489249925092519252925392549255925692579258925992609261926292639264926592669267926892699270927192729273927492759276927792789279928092819282928392849285928692879288928992909291929292939294929592969297929892999300930193029303930493059306930793089309931093119312931393149315931693179318931993209321932293239324932593269327932893299330933193329333933493359336933793389339934093419342934393449345934693479348934993509351935293539354935593569357935893599360936193629363936493659366936793689369937093719372937393749375937693779378937993809381938293839384938593869387938893899390939193929393939493959396939793989399940094019402940394049405940694079408940994109411941294139414941594169417941894199420942194229423942494259426942794289429943094319432943394349435943694379438943994409441944294439444944594469447944894499450945194529453945494559456945794589459946094619462946394649465946694679468946994709471947294739474947594769477947894799480948194829483948494859486948794889489949094919492949394949495949694979498949995009501950295039504950595069507950895099510951195129513951495159516951795189519952095219522952395249525952695279528952995309531953295339534953595369537953895399540954195429543954495459546954795489549955095519552955395549555955695579558955995609561956295639564956595669567956895699570957195729573957495759576957795789579958095819582958395849585958695879588958995909591959295939594959595969597959895999600960196029603960496059606960796089609961096119612961396149615961696179618961996209621962296239624962596269627962896299630963196329633963496359636963796389639964096419642964396449645964696479648964996509651965296539654965596569657965896599660966196629663966496659666966796689669967096719672967396749675967696779678967996809681968296839684968596869687968896899690969196929693969496959696969796989699970097019702970397049705970697079708970997109711971297139714971597169717971897199720972197229723972497259726972797289729973097319732973397349735973697379738973997409741974297439744974597469747974897499750975197529753975497559756975797589759976097619762976397649765976697679768976997709771977297739774977597769777977897799780978197829783978497859786978797889789979097919792979397949795979697979798979998009801980298039804980598069807980898099810981198129813981498159816981798189819982098219822982398249825982698279828982998309831983298339834983598369837983898399840984198429843984498459846984798489849985098519852985398549855985698579858985998609861986298639864986598669867986898699870987198729873987498759876987798789879988098819882988398849885988698879888988998909891989298939894989598969897989898999900990199029903990499059906990799089909991099119912991399149915991699179918991999209921992299239924992599269927992899299930993199329933993499359936993799389939994099419942994399449945994699479948994999509951995299539954995599569957995899599960996199629963996499659966996799689969997099719972997399749975997699779978997999809981998299839984998599869987998899899990999199929993999499959996999799989999100001000110002100031000410005100061000710008100091001010011100121001310014100151001610017100181001910020100211002210023100241002510026100271002810029100301003110032100331003410035100361003710038100391004010041100421004310044100451004610047100481004910050100511005210053100541005510056100571005810059100601006110062100631006410065100661006710068100691007010071100721007310074100751007610077100781007910080100811008210083100841008510086100871008810089100901009110092100931009410095100961009710098100991010010101101021010310104101051010610107101081010910110101111011210113101141011510116101171011810119101201012110122101231012410125101261012710128101291013010131101321013310134101351013610137101381013910140101411014210143101441014510146101471014810149101501015110152101531015410155101561015710158101591016010161101621016310164101651016610167101681016910170101711017210173101741017510176101771017810179101801018110182101831018410185101861018710188101891019010191101921019310194101951019610197101981019910200102011020210203102041020510206102071020810209102101021110212102131021410215102161021710218102191022010221102221022310224102251022610227102281022910230102311023210233102341023510236102371023810239102401024110242102431024410245102461024710248102491025010251102521025310254102551025610257102581025910260102611026210263102641026510266102671026810269102701027110272102731027410275102761027710278102791028010281102821028310284102851028610287102881028910290102911029210293102941029510296102971029810299103001030110302103031030410305103061030710308103091031010311103121031310314103151031610317103181031910320103211032210323103241032510326103271032810329103301033110332103331033410335103361033710338103391034010341103421034310344103451034610347103481034910350103511035210353103541035510356103571035810359103601036110362103631036410365103661036710368103691037010371103721037310374103751037610377103781037910380103811038210383103841038510386103871038810389103901039110392103931039410395103961039710398103991040010401104021040310404104051040610407104081040910410104111041210413104141041510416104171041810419104201042110422104231042410425104261042710428104291043010431104321043310434104351043610437104381043910440104411044210443104441044510446104471044810449104501045110452104531045410455104561045710458104591046010461104621046310464104651046610467104681046910470104711047210473104741047510476104771047810479104801048110482104831048410485104861048710488104891049010491104921049310494104951049610497104981049910500105011050210503105041050510506105071050810509105101051110512105131051410515105161051710518105191052010521105221052310524105251052610527105281052910530105311053210533105341053510536105371053810539105401054110542105431054410545105461054710548105491055010551105521055310554105551055610557105581055910560105611056210563105641056510566105671056810569105701057110572105731057410575105761057710578105791058010581105821058310584105851058610587105881058910590105911059210593105941059510596105971059810599106001060110602106031060410605106061060710608106091061010611106121061310614106151061610617106181061910620106211062210623106241062510626106271062810629106301063110632106331063410635106361063710638106391064010641106421064310644106451064610647106481064910650106511065210653106541065510656106571065810659106601066110662106631066410665106661066710668106691067010671106721067310674106751067610677106781067910680106811068210683106841068510686106871068810689106901069110692106931069410695106961069710698106991070010701107021070310704107051070610707107081070910710107111071210713107141071510716107171071810719107201072110722107231072410725107261072710728107291073010731107321073310734107351073610737107381073910740107411074210743 |
- Thu Aug 8 10:54:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub004/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub004/anatomy/other/t2w001.nii.gz -T2pial -subjid sub004 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub004
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Actual FREESURFER_HOME /opt/freesurfer/5.3.0
- build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- cputime unlimited
- filesize unlimited
- datasize unlimited
- stacksize unlimited
- coredumpsize 0 kbytes
- memoryuse unlimited
- vmemoryuse unlimited
- descriptors 1024
- memorylocked 64 kbytes
- maxproc unlimited
- maxlocks unlimited
- maxsignal 16382
- maxmessage 819200
- maxnice 0
- maxrtprio 0
- maxrttime unlimited
- total used free shared buffers cached
- Mem: 99201692 96849752 2351940 0 177164 93992360
- -/+ buffers/cache: 2680228 96521464
- Swap: 25165780 3620 25162160
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ======= NUMBER OF OPENMP THREADS = 1 =======
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
- ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- #######################################
- GCADIR /opt/freesurfer/5.3.0/average
- GCA RB_all_2008-03-26.gca
- GCASkull RB_all_withskull_2008-03-26.gca
- AvgCurvTif average.curvature.filled.buckner40.tif
- GCSDIR /opt/freesurfer/5.3.0/average
- GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
- #######################################
- -cw256 option is now persistent (remove with -clean-cw256)
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub004/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub004/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/001.mgz
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from /home/data/exppsy/forrest_gump/openfmri.org/sub004/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996814, 0.0369416, 0.0706971)
- j_ras = (0.0317143, 0.996777, -0.0736842)
- k_ras = (0.0731912, 0.0712073, 0.994773)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub004/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub004/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from /home/data/exppsy/forrest_gump/openfmri.org/sub004/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996814, 0.0369416, 0.0706971)
- j_ras = (0.0317143, 0.996777, -0.0736842)
- k_ras = (0.0731912, 0.0712073, 0.994773)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:55 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/001.mgz
- Checking for (invalid) multi-frame inputs...
- WARNING: only one run found. This is OK, but motion
- correction cannot be performed on one run, so I'll
- copy the run to rawavg and continue.
- cp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz --conform --cw256
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996814, 0.0369416, 0.0706971)
- j_ras = (0.0317143, 0.996777, -0.0736842)
- k_ras = (0.0731912, 0.0712073, 0.994773)
- Original Data has (0.699951, 0.666667, 0.666667) mm size and (274, 384, 384) voxels.
- Data is conformed to 1 mm size and 256 voxels for all directions
- changing data type from float to uchar (noscale = 0)...
- MRIchangeType: Building histogram
- Reslicing using trilinear interpolation
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:58:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7961, pval=0.8469 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/talairach_avi.log
- TalAviQA: 0.96758
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:58:37 CEST 2013
- mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni
- --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- nIters 2
- $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:58:37 CEST 2013
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- tmpdir is ./tmp.mri_nu_correct.mni.14570
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14570/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14570/nu0.mnc -odt float
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from orig.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -5.58794e-09, -7.45058e-09)
- j_ras = (7.45058e-09, 1.49012e-08, -1)
- k_ras = (-1.86265e-09, 1, 7.45058e-09)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.14570/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:41 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.14570/nu0.mnc ./tmp.mri_nu_correct.mni.14570/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14570/0/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/] [2013-08-08 10:58:42] running:
- /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.14570/0/ ./tmp.mri_nu_correct.mni.14570/nu0.mnc ./tmp.mri_nu_correct.mni.14570/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 47
- CV of field change: 0.000997356
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/] [2013-08-08 11:00:00] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14570/nu0.mnc ./tmp.mri_nu_correct.mni.14570/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 11:00:07 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.14570/nu1.mnc ./tmp.mri_nu_correct.mni.14570/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.14570/1/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/] [2013-08-08 11:00:08] running:
- /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.14570/1/ ./tmp.mri_nu_correct.mni.14570/nu1.mnc ./tmp.mri_nu_correct.mni.14570/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 23
- CV of field change: 0.000984184
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/] [2013-08-08 11:00:40] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14570/nu1.mnc ./tmp.mri_nu_correct.mni.14570/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.14570/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14570/ones.mgz
- $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
- cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.14570/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14570/ones.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.14570/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.14570/ones.mgz
- Binarizing based on threshold
- min -1
- max +infinity
- binval 1
- binvalnot 0
- Found 16777216 values in range
- Counting number of voxels
- Found 16777216 voxels in final mask
- mri_binarize done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14570/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14570/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14570/input.mean.dat
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14570/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14570/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14570/input.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.14570/ones.mgz
- Loading orig.mgz
- Voxel Volume is 1 mm^3
- Generating list of segmentation ids
- Found 1 segmentations
- Computing statistics for each segmentation
- 0 1 16777216 16777216.000
- Reporting on 1 segmentations
- Computing spatial average of each frame
- 0
- Writing to ./tmp.mri_nu_correct.mni.14570/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14570/ones.mgz --i ./tmp.mri_nu_correct.mni.14570/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14570/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14570/output.mean.dat
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14570/ones.mgz --i ./tmp.mri_nu_correct.mni.14570/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14570/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14570/output.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.14570/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.14570/nu2.mnc
- Voxel Volume is 1 mm^3
- Generating list of segmentation ids
- Found 1 segmentations
- Computing statistics for each segmentation
- 0 1 16777216 16777216.000
- Reporting on 1 segmentations
- Computing spatial average of each frame
- 0
- Writing to ./tmp.mri_nu_correct.mni.14570/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.14570/nu2.mnc ./tmp.mri_nu_correct.mni.14570/nu2.mnc mul .92767722663627935008
- Saving result to './tmp.mri_nu_correct.mni.14570/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.14570/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.14570/nu2.mnc nu.mgz --like orig.mgz
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from ./tmp.mri_nu_correct.mni.14570/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -5.58794e-09, -7.45058e-09)
- j_ras = (7.45058e-09, 1.49012e-08, -1)
- k_ras = (-1.86265e-09, 1, 7.45058e-09)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 8 seconds.
- mapping ( 9, 181) to ( 3, 110)
-
-
- Thu Aug 8 11:01:40 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:01:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.135 -0.026 -0.050 3.076;
- 0.004 1.151 0.129 -45.572;
- 0.048 -0.293 1.265 -38.522;
- 0.000 0.000 0.000 1.000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 16
- Starting OpenSpline(): npoints = 16
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 56 (56), valley at 36 (36)
- csf peak at 12, setting threshold to 41
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 57 (57), valley at 36 (36)
- csf peak at 12, setting threshold to 42
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 48 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:04:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- reading 1 input volumes...
- logging results to talairach_with_skull.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=8.0
- skull bounding box = (55, 19, 26) --> (199, 255, 150)
- using (103, 98, 88) as brain centroid...
- mean wm in atlas = 126, using box (85,69,73) --> (120, 127,103) to find MRI wm
- before smoothing, mri peak at 113
- after smoothing, mri peak at 113, scaling input intensities by 1.115
- scaling channel 0 by 1.11504
- initial log_p = -4.8
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.564661 @ (-9.091, 9.091, -9.091)
- max log p = -4.383550 @ (4.545, 13.636, -4.545)
- max log p = -4.323476 @ (2.273, -2.273, -2.273)
- max log p = -4.323476 @ (0.000, 0.000, 0.000)
- max log p = -4.316703 @ (2.841, -0.568, 0.568)
- max log p = -4.304100 @ (-0.852, -0.852, 0.284)
- Found translation: (-0.3, 19.0, -15.1): log p = -4.304
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.3 (thresh=-4.3)
- 1.064 0.000 0.000 -8.319;
- 0.000 1.226 0.140 -13.493;
- 0.000 -0.161 1.066 -6.554;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.064 0.000 0.000 -8.319;
- 0.000 1.318 0.151 -23.589;
- 0.000 -0.161 1.066 -6.554;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.083 -0.011 0.033 -13.728;
- 0.005 1.367 0.157 -31.492;
- -0.038 -0.170 1.126 -8.360;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.083 -0.011 0.033 -13.728;
- 0.005 1.367 0.157 -31.492;
- -0.038 -0.170 1.126 -8.360;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.087 -0.010 0.024 -13.273;
- 0.005 1.369 0.157 -31.671;
- -0.029 -0.170 1.125 -8.890;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.087 -0.010 0.024 -13.273;
- 0.005 1.369 0.157 -31.671;
- -0.029 -0.170 1.123 -8.756;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 3481 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.08728 -0.00953 0.02424 -13.27257;
- 0.00473 1.36858 0.15683 -31.67060;
- -0.02905 -0.17013 1.12342 -8.75576;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.08728 -0.00953 0.02424 -13.27257;
- 0.00473 1.36858 0.15683 -31.67060;
- -0.02905 -0.17013 1.12342 -8.75576;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.087 -0.010 0.024 -13.273;
- 0.005 1.369 0.157 -31.671;
- -0.029 -0.170 1.123 -8.756;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.8)
- transform before final EM align:
- 1.087 -0.010 0.024 -13.273;
- 0.005 1.369 0.157 -31.671;
- -0.029 -0.170 1.123 -8.756;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 382743 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.08728 -0.00953 0.02424 -13.27257;
- 0.00473 1.36858 0.15683 -31.67060;
- -0.02905 -0.17013 1.12342 -8.75576;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.08728 -0.00953 0.02424 -13.27257;
- 0.00473 1.36858 0.15683 -31.67060;
- -0.02905 -0.17013 1.12342 -8.75576;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.087 -0.010 0.024 -13.273;
- 0.005 1.369 0.157 -31.671;
- -0.029 -0.170 1.123 -8.756;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 29 minutes and 33 seconds.
- mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
- Mode: T1 normalized volume
- Mode: Use the information of atlas (default parms, --help for details)
- *********************************************************
- The input file is T1.mgz
- The output file is brainmask.auto.mgz
- Weighting the input with atlas information before watershed
- *************************WATERSHED**************************
- Sorting...
- first estimation of the COG coord: x=125 y=87 z=125 r=89
- first estimation of the main basin volume: 2995932 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 15 found in the rest of the brain
- global maximum in x=147, y=83, z=87, Imax=255
- CSF=12, WM_intensity=110, WM_VARIANCE=5
- WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
- preflooding height equal to 10 percent
- done.
- Analyze...
- main basin size=19001794123 voxels, voxel volume =1.000
- = 19001794123 mmm3 = 19001794.560 cm3
- done.
- PostAnalyze...Basin Prior
- 94 basins merged thanks to atlas
- ***** 0 basin(s) merged in 1 iteration(s)
- ***** 0 voxel(s) added to the main basin
- done.
- Weighting the input with prior template
- ****************TEMPLATE DEFORMATION****************
- second estimation of the COG coord: x=126,y=98, z=117, r=9263 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 45188
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = -1044668778
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1096399820
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 1045649112
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 1075314790
- OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=38 , nb = 1075670866
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 6, 9, 29, 50
- after analyzing : 6, 22, 29, 29
- RIGHT_CER
- before analyzing : 18, 23, 32, 54
- after analyzing : 18, 29, 32, 35
- LEFT_CER
- before analyzing : 24, 21, 17, 61
- after analyzing : 21, 23, 25, 32
- RIGHT_BRAIN
- before analyzing : 6, 9, 27, 50
- after analyzing : 6, 21, 27, 28
- LEFT_BRAIN
- before analyzing : 6, 9, 28, 50
- after analyzing : 6, 21, 28, 28
- OTHER
- before analyzing : 38, 32, 29, 50
- after analyzing : 24, 32, 32, 36
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...64 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.011
- curvature mean = 69.812, std = 8.616
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 1.90, sigma = 2.95
- after rotation: sse = 1.90, sigma = 2.95
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 1.97, its var is 2.51
- before Erosion-Dilatation 0.11% of inacurate vertices
- after Erosion-Dilatation 0.00% of inacurate vertices
- Validation of the shape of the surface done.
- Scaling of atlas fields onto current surface fields
- ********FINAL ITERATIVE TEMPLATE DEFORMATION********
- Compute Local values csf/gray
- Fine Segmentation...44 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1633705 voxels, voxel volume = 1.000 mm3
- = 1633705 mmm3 = 1633.705 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:34:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 3
- using MR volume brainmask.mgz to mask input volume...
- reading 1 input volumes...
- logging results to talairach.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'...
- average std = 6.9 using min determinant for regularization = 4.7
- 0 singular and 1812 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 14.9 or > 790.2
- total sample mean = 84.4 (994 zeros)
- ************************************************
- spacing=8, using 2772 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 2772, passno 0, spacing 8
- resetting wm mean[0]: 102 --> 107
- resetting gm mean[0]: 64 --> 64
- input volume #1 is the most T1-like
- using real data threshold=22.0
- skull bounding box = (59, 43, 41) --> (193, 153, 205)
- using (104, 80, 123) as brain centroid...
- mean wm in atlas = 107, using box (88,67,103) --> (120, 93,143) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 108, scaling input intensities by 0.991
- scaling channel 0 by 0.990741
- initial log_p = -4.5
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -3.994477 @ (-9.091, 27.273, -9.091)
- max log p = -3.776515 @ (4.545, -4.545, -4.545)
- max log p = -3.711429 @ (2.273, -2.273, -2.273)
- max log p = -3.694539 @ (-1.136, 1.136, -3.409)
- max log p = -3.668388 @ (-1.705, -0.568, 1.705)
- max log p = -3.668388 @ (0.000, 0.000, 0.000)
- Found translation: (-5.1, 21.0, -17.6): log p = -3.668
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.7 (thresh=-3.7)
- 1.150 0.000 0.000 -24.902;
- 0.000 1.075 0.000 13.685;
- 0.000 0.000 1.000 -17.614;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6)
- 1.150 0.000 0.000 -24.902;
- 0.000 1.146 0.140 -10.487;
- 0.000 -0.140 0.991 4.667;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.6 (thresh=-3.6)
- 1.150 0.000 0.000 -24.902;
- 0.000 1.068 0.009 12.391;
- 0.000 0.010 1.001 -18.856;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
- 1.150 0.000 0.000 -24.902;
- 0.000 1.068 0.009 12.391;
- 0.000 0.010 1.001 -18.856;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.5 (thresh=-3.5)
- 1.085 -0.034 0.025 -12.459;
- 0.042 1.119 0.151 -12.044;
- -0.040 -0.134 1.009 3.580;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.085 -0.034 0.025 -12.459;
- 0.043 1.139 0.154 -14.407;
- -0.040 -0.134 1.009 3.580;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.085 -0.034 0.025 -12.459;
- 0.043 1.139 0.154 -14.407;
- -0.040 -0.134 1.009 3.580;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3)
- 1.084 -0.025 0.027 -13.375;
- 0.034 1.138 0.162 -14.581;
- -0.040 -0.143 1.009 4.085;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.084 -0.025 0.027 -13.375;
- 0.034 1.138 0.162 -14.581;
- -0.040 -0.143 1.009 4.085;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 2772 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.08427 -0.02479 0.02670 -13.37477;
- 0.03421 1.13835 0.16169 -14.58101;
- -0.04029 -0.14306 1.00910 4.08530;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.08427 -0.02479 0.02670 -13.37477;
- 0.03421 1.13835 0.16169 -14.58101;
- -0.04029 -0.14306 1.00910 4.08530;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.084 -0.025 0.027 -13.375;
- 0.034 1.138 0.162 -14.581;
- -0.040 -0.143 1.009 4.085;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.2 (old=-4.5)
- transform before final EM align:
- 1.084 -0.025 0.027 -13.375;
- 0.034 1.138 0.162 -14.581;
- -0.040 -0.143 1.009 4.085;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 312841 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.08427 -0.02479 0.02670 -13.37477;
- 0.03421 1.13835 0.16169 -14.58101;
- -0.04029 -0.14306 1.00910 4.08530;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.08427 -0.02479 0.02670 -13.37477;
- 0.03421 1.13835 0.16169 -14.58101;
- -0.04029 -0.14306 1.00910 4.08530;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 3.8 tol 0.000000
- final transform:
- 1.084 -0.025 0.027 -13.375;
- 0.034 1.138 0.162 -14.581;
- -0.040 -0.143 1.009 4.085;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 35 minutes and 11 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:09:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
- writing control point volume to ctrl_pts.mgz
- using MR volume brainmask.mgz to mask input volume...
- reading 1 input volume
- reading atlas from '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'...
- reading transform from 'transforms/talairach.lta'...
- reading input volume from nu.mgz...
- resetting wm mean[0]: 102 --> 107
- resetting gm mean[0]: 64 --> 64
- input volume #1 is the most T1-like
- using real data threshold=22.0
- skull bounding box = (59, 43, 40) --> (193, 153, 205)
- using (104, 80, 123) as brain centroid...
- mean wm in atlas = 107, using box (88,67,103) --> (120, 93,143) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 108, scaling input intensities by 0.991
- scaling channel 0 by 0.990741
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.084 -0.025 0.027 -13.375;
- 0.034 1.138 0.162 -14.581;
- -0.040 -0.143 1.009 4.085;
- 0.000 0.000 0.000 1.000;
- INFO: transform used
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (128, 38, 43) --> (189, 137, 207)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 144.0
- 0 of 95 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (68, 40, 42) --> (128, 140, 206)
- Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 144.0
- 0 of 69 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 114, 69) --> (176, 152, 121)
- Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 144.0
- 5 of 18 (27.8%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 114, 66) --> (130, 153, 121)
- Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 144.0
- 0 of 11 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 106, 102) --> (143, 167, 132)
- Brain_Stem: limiting intensities to 77.0 --> 144.0
- 0 of 11 (0.0%) samples deleted
- using 204 total control points for intensity normalization...
- bias field = 0.982 +- 0.060
- 0 of 199 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (128, 38, 43) --> (189, 137, 207)
- Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 134.0
- 0 of 144 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (68, 40, 42) --> (128, 140, 206)
- Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 134.0
- 0 of 115 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 114, 69) --> (176, 152, 121)
- Left_Cerebellum_White_Matter: limiting intensities to 78.0 --> 134.0
- 0 of 34 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 114, 66) --> (130, 153, 121)
- Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 134.0
- 1 of 43 (2.3%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 106, 102) --> (143, 167, 132)
- Brain_Stem: limiting intensities to 70.0 --> 134.0
- 0 of 60 (0.0%) samples deleted
- using 396 total control points for intensity normalization...
- bias field = 1.008 +- 0.057
- 0 of 395 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (128, 38, 43) --> (189, 137, 207)
- Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 135.0
- 0 of 243 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (68, 40, 42) --> (128, 140, 206)
- Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 135.0
- 0 of 201 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 114, 69) --> (176, 152, 121)
- Left_Cerebellum_White_Matter: limiting intensities to 74.0 --> 135.0
- 0 of 57 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 114, 66) --> (130, 153, 121)
- Right_Cerebellum_White_Matter: limiting intensities to 75.0 --> 135.0
- 0 of 31 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 106, 102) --> (143, 167, 132)
- Brain_Stem: limiting intensities to 66.0 --> 135.0
- 0 of 131 (0.0%) samples deleted
- using 663 total control points for intensity normalization...
- bias field = 1.019 +- 0.054
- 1 of 663 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 5 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:11:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.m3z
- not handling expanded ventricles...
- using previously computed transform transforms/talairach.lta
- renormalizing sequences with structure alignment, equivalent to:
- -renormalize
- -regularize_mean 0.500
- -regularize 0.500
- using MR volume brainmask.mgz to mask input volume...
- reading 1 input volumes...
- logging results to talairach.log
- ======= NUMBER OF OPENMP THREADS = 1 =======
- reading input volume 'norm.mgz'...
- reading GCA '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'...
- label assignment complete, 0 changed (0.00%)
- det(m_affine) = 1.27 (predicted orig area = 6.3)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.867, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.762 (12.180%), neg=0, invalid=96777
- 0002: dt=221.952000, rms=0.732 (3.837%), neg=0, invalid=96777
- 0003: dt=129.472000, rms=0.725 (1.024%), neg=0, invalid=96777
- 0004: dt=295.936000, rms=0.718 (0.947%), neg=0, invalid=96777
- 0005: dt=73.984000, rms=0.714 (0.558%), neg=0, invalid=96777
- 0006: dt=443.904000, rms=0.708 (0.812%), neg=0, invalid=96777
- 0007: dt=73.984000, rms=0.706 (0.346%), neg=0, invalid=96777
- 0008: dt=517.888000, rms=0.702 (0.605%), neg=0, invalid=96777
- 0009: dt=73.984000, rms=0.700 (0.168%), neg=0, invalid=96777
- 0010: dt=73.984000, rms=0.700 (0.114%), neg=0, invalid=96777
- 0011: dt=73.984000, rms=0.698 (0.156%), neg=0, invalid=96777
- 0012: dt=73.984000, rms=0.697 (0.181%), neg=0, invalid=96777
- 0013: dt=73.984000, rms=0.696 (0.192%), neg=0, invalid=96777
- 0014: dt=73.984000, rms=0.694 (0.240%), neg=0, invalid=96777
- 0015: dt=73.984000, rms=0.692 (0.252%), neg=0, invalid=96777
- 0016: dt=73.984000, rms=0.691 (0.247%), neg=0, invalid=96777
- 0017: dt=73.984000, rms=0.689 (0.238%), neg=0, invalid=96777
- 0018: dt=73.984000, rms=0.688 (0.209%), neg=0, invalid=96777
- 0019: dt=73.984000, rms=0.686 (0.195%), neg=0, invalid=96777
- 0020: dt=73.984000, rms=0.685 (0.198%), neg=0, invalid=96777
- 0021: dt=73.984000, rms=0.684 (0.170%), neg=0, invalid=96777
- 0022: dt=73.984000, rms=0.683 (0.145%), neg=0, invalid=96777
- 0023: dt=73.984000, rms=0.682 (0.133%), neg=0, invalid=96777
- 0024: dt=73.984000, rms=0.681 (0.099%), neg=0, invalid=96777
- 0025: dt=73.984000, rms=0.680 (0.130%), neg=0, invalid=96777
- 0026: dt=73.984000, rms=0.679 (0.126%), neg=0, invalid=96777
- 0027: dt=73.984000, rms=0.679 (0.105%), neg=0, invalid=96777
- 0028: dt=73.984000, rms=0.678 (0.097%), neg=0, invalid=96777
- 0029: dt=295.936000, rms=0.678 (0.024%), neg=0, invalid=96777
- 0030: dt=295.936000, rms=0.677 (0.066%), neg=0, invalid=96777
- 0031: dt=295.936000, rms=0.678 (-0.578%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.678, neg=0, invalid=96777
- 0032: dt=32.368000, rms=0.677 (0.054%), neg=0, invalid=96777
- 0033: dt=32.368000, rms=0.677 (0.020%), neg=0, invalid=96777
- 0034: dt=32.368000, rms=0.677 (0.011%), neg=0, invalid=96777
- 0035: dt=32.368000, rms=0.677 (0.007%), neg=0, invalid=96777
- 0036: dt=32.368000, rms=0.677 (0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.681, neg=0, invalid=96777
- 0037: dt=145.152000, rms=0.665 (2.330%), neg=0, invalid=96777
- 0038: dt=20.736000, rms=0.663 (0.304%), neg=0, invalid=96777
- 0039: dt=145.152000, rms=0.653 (1.528%), neg=0, invalid=96777
- 0040: dt=36.288000, rms=0.649 (0.618%), neg=0, invalid=96777
- 0041: dt=145.152000, rms=0.644 (0.733%), neg=0, invalid=96777
- 0042: dt=36.288000, rms=0.641 (0.545%), neg=0, invalid=96777
- 0043: dt=62.208000, rms=0.639 (0.285%), neg=0, invalid=96777
- 0044: dt=36.288000, rms=0.637 (0.295%), neg=0, invalid=96777
- 0045: dt=62.208000, rms=0.635 (0.289%), neg=0, invalid=96777
- 0046: dt=31.104000, rms=0.634 (0.174%), neg=0, invalid=96777
- 0047: dt=31.104000, rms=0.633 (0.211%), neg=0, invalid=96777
- 0048: dt=31.104000, rms=0.631 (0.269%), neg=0, invalid=96777
- 0049: dt=31.104000, rms=0.629 (0.343%), neg=0, invalid=96777
- 0050: dt=31.104000, rms=0.627 (0.404%), neg=0, invalid=96777
- 0051: dt=31.104000, rms=0.624 (0.489%), neg=0, invalid=96777
- 0052: dt=31.104000, rms=0.620 (0.505%), neg=0, invalid=96777
- 0053: dt=31.104000, rms=0.617 (0.462%), neg=0, invalid=96777
- 0054: dt=31.104000, rms=0.615 (0.433%), neg=0, invalid=96777
- 0055: dt=31.104000, rms=0.612 (0.384%), neg=0, invalid=96777
- 0056: dt=31.104000, rms=0.610 (0.389%), neg=0, invalid=96777
- 0057: dt=31.104000, rms=0.608 (0.327%), neg=0, invalid=96777
- 0058: dt=31.104000, rms=0.607 (0.256%), neg=0, invalid=96777
- 0059: dt=31.104000, rms=0.605 (0.226%), neg=0, invalid=96777
- 0060: dt=31.104000, rms=0.604 (0.205%), neg=0, invalid=96777
- 0061: dt=31.104000, rms=0.603 (0.214%), neg=0, invalid=96777
- 0062: dt=31.104000, rms=0.602 (0.149%), neg=0, invalid=96777
- 0063: dt=31.104000, rms=0.601 (0.097%), neg=0, invalid=96777
- 0064: dt=31.104000, rms=0.601 (0.078%), neg=0, invalid=96777
- 0065: dt=82.944000, rms=0.600 (0.087%), neg=0, invalid=96777
- 0066: dt=6.480000, rms=0.600 (-0.006%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.600, neg=0, invalid=96777
- 0067: dt=9.072000, rms=0.600 (0.032%), neg=0, invalid=96777
- 0068: dt=9.072000, rms=0.600 (0.019%), neg=0, invalid=96777
- 0069: dt=9.072000, rms=0.600 (0.014%), neg=0, invalid=96777
- 0070: dt=9.072000, rms=0.600 (0.001%), neg=0, invalid=96777
- 0071: dt=9.072000, rms=0.600 (-0.015%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.625, neg=0, invalid=96777
- 0072: dt=8.000000, rms=0.624 (0.131%), neg=0, invalid=96777
- 0073: dt=3.333333, rms=0.624 (0.011%), neg=0, invalid=96777
- 0074: dt=3.333333, rms=0.624 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.624, neg=0, invalid=96777
- 0075: dt=0.000000, rms=0.624 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.689, neg=0, invalid=96777
- 0076: dt=5.381579, rms=0.672 (2.458%), neg=0, invalid=96777
- 0077: dt=1.886792, rms=0.671 (0.053%), neg=0, invalid=96777
- 0078: dt=1.886792, rms=0.671 (0.001%), neg=0, invalid=96777
- 0079: dt=1.886792, rms=0.671 (-0.155%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.671, neg=0, invalid=96777
- 0080: dt=0.000000, rms=0.671 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 5.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.734, neg=0, invalid=96777
- 0081: dt=0.617647, rms=0.733 (0.216%), neg=0, invalid=96777
- 0082: dt=1.280000, rms=0.730 (0.287%), neg=0, invalid=96777
- 0083: dt=1.918605, rms=0.728 (0.336%), neg=0, invalid=96777
- 0084: dt=0.448000, rms=0.728 (0.019%), neg=0, invalid=96777
- 0085: dt=0.448000, rms=0.728 (0.015%), neg=0, invalid=96777
- 0086: dt=0.448000, rms=0.728 (0.006%), neg=0, invalid=96777
- 0087: dt=0.448000, rms=0.728 (-0.027%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.728, neg=0, invalid=96777
- 0088: dt=1.282609, rms=0.727 (0.154%), neg=0, invalid=96777
- 0089: dt=0.000000, rms=0.727 (-0.002%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 10.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.679, neg=0, invalid=96777
- 0090: dt=0.152941, rms=0.672 (1.097%), neg=0, invalid=96777
- 0091: dt=0.000000, rms=0.672 (0.006%), neg=0, invalid=96777
- 0092: dt=0.050000, rms=0.672 (-0.011%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.672, neg=0, invalid=96777
- 0093: dt=0.028000, rms=0.671 (0.072%), neg=0, invalid=96777
- 0094: dt=0.112000, rms=0.670 (0.203%), neg=0, invalid=96777
- 0095: dt=0.112000, rms=0.669 (0.100%), neg=0, invalid=96777
- 0096: dt=0.112000, rms=0.668 (0.078%), neg=0, invalid=96777
- 0097: dt=0.112000, rms=0.668 (0.135%), neg=0, invalid=96777
- 0098: dt=0.112000, rms=0.666 (0.162%), neg=0, invalid=96777
- 0099: dt=0.112000, rms=0.666 (0.020%), neg=0, invalid=96777
- 0100: dt=0.112000, rms=0.666 (0.038%), neg=0, invalid=96777
- 0101: dt=0.112000, rms=0.666 (0.059%), neg=0, invalid=96777
- 0102: dt=0.112000, rms=0.666 (0.025%), neg=0, invalid=96777
- 0103: dt=0.112000, rms=0.665 (0.021%), neg=0, invalid=96777
- 0104: dt=0.112000, rms=0.665 (0.018%), neg=0, invalid=96777
- 0105: dt=0.028000, rms=0.665 (0.004%), neg=0, invalid=96777
- 0106: dt=0.028000, rms=0.665 (0.004%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.07025 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.26 x + 0.0 (1495 voxels, overlap=0.391)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1495 voxels, peak = 6), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.10428 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.37 x + 0.0 (655 voxels, overlap=0.008)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (655 voxels, peak = 8), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.09472 (92)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (393 voxels, overlap=0.042)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (393 voxels, peak = 92), gca=91.5
- gca peak = 0.19192 (97)
- mri peak = 0.08533 (79)
- Left_Pallidum (13): linear fit = 0.82 x + 0.0 (223 voxels, overlap=0.042)
- Left_Pallidum (13): linear fit = 0.82 x + 0.0 (223 voxels, peak = 80), gca=80.0
- gca peak = 0.24007 (63)
- mri peak = 0.07489 (57)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (583 voxels, overlap=0.803)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (583 voxels, peak = 55), gca=55.1
- gca peak = 0.29892 (64)
- mri peak = 0.10161 (57)
- Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (533 voxels, overlap=0.742)
- Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (533 voxels, peak = 56), gca=56.0
- gca peak = 0.12541 (104)
- mri peak = 0.08566 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (62042 voxels, overlap=0.760)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (62042 voxels, peak = 108), gca=107.6
- gca peak = 0.13686 (104)
- mri peak = 0.08419 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (64505 voxels, overlap=0.713)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (64505 voxels, peak = 108), gca=107.6
- gca peak = 0.11691 (63)
- mri peak = 0.05434 (51)
- Left_Cerebral_Cortex (3): linear fit = 0.81 x + 0.0 (18476 voxels, overlap=0.186)
- Left_Cerebral_Cortex (3): linear fit = 0.81 x + 0.0 (18476 voxels, peak = 51), gca=51.3
- gca peak = 0.13270 (63)
- mri peak = 0.04901 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (20076 voxels, overlap=0.110)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (20076 voxels, peak = 50), gca=50.1
- gca peak = 0.15182 (70)
- mri peak = 0.08238 (68)
- Right_Caudate (50): linear fit = 0.92 x + 0.0 (445 voxels, overlap=0.606)
- Right_Caudate (50): linear fit = 0.92 x + 0.0 (445 voxels, peak = 64), gca=64.1
- gca peak = 0.14251 (76)
- mri peak = 0.05200 (66)
- Left_Caudate (11): linear fit = 0.83 x + 0.0 (559 voxels, overlap=0.345)
- Left_Caudate (11): linear fit = 0.83 x + 0.0 (559 voxels, peak = 63), gca=63.5
- gca peak = 0.12116 (60)
- mri peak = 0.04362 (57)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (13112 voxels, overlap=0.989)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (13112 voxels, peak = 58), gca=57.9
- gca peak = 0.12723 (61)
- mri peak = 0.04317 (53)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (15080 voxels, overlap=0.925)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (15080 voxels, peak = 57), gca=57.0
- gca peak = 0.22684 (88)
- mri peak = 0.06242 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6199 voxels, overlap=0.949)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6199 voxels, peak = 90), gca=90.2
- gca peak = 0.21067 (87)
- mri peak = 0.06488 (84)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5645 voxels, overlap=0.982)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5645 voxels, peak = 88), gca=88.3
- gca peak = 0.25455 (62)
- mri peak = 0.06522 (64)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (326 voxels, overlap=0.994)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (326 voxels, peak = 58), gca=58.0
- gca peak = 0.39668 (62)
- mri peak = 0.07975 (60)
- Right_Amygdala (54): linear fit = 0.95 x + 0.0 (332 voxels, overlap=1.004)
- Right_Amygdala (54): linear fit = 0.95 x + 0.0 (332 voxels, peak = 59), gca=59.2
- gca peak = 0.10129 (93)
- mri peak = 0.05187 (90)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (5206 voxels, overlap=0.998)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (5206 voxels, peak = 90), gca=89.7
- gca peak = 0.12071 (89)
- mri peak = 0.06295 (80)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (4082 voxels, overlap=0.796)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (4082 voxels, peak = 83), gca=83.2
- gca peak = 0.13716 (82)
- mri peak = 0.05013 (78)
- Left_Putamen (12): linear fit = 0.96 x + 0.0 (1888 voxels, overlap=0.992)
- Left_Putamen (12): linear fit = 0.96 x + 0.0 (1888 voxels, peak = 79), gca=79.1
- gca peak = 0.15214 (84)
- mri peak = 0.06170 (76)
- Right_Putamen (51): linear fit = 0.93 x + 0.0 (1889 voxels, overlap=0.552)
- Right_Putamen (51): linear fit = 0.93 x + 0.0 (1889 voxels, peak = 78), gca=77.7
- gca peak = 0.08983 (85)
- mri peak = 0.09325 (84)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (9638 voxels, overlap=0.777)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (9638 voxels, peak = 87), gca=87.1
- gca peak = 0.11809 (92)
- mri peak = 0.08257 (89)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (630 voxels, overlap=0.874)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (630 voxels, peak = 89), gca=88.8
- gca peak = 0.12914 (94)
- mri peak = 0.06677 (89)
- Left_VentralDC (28): linear fit = 0.95 x + 0.0 (917 voxels, overlap=0.946)
- Left_VentralDC (28): linear fit = 0.95 x + 0.0 (917 voxels, peak = 90), gca=89.8
- gca peak = 0.21100 (36)
- mri peak = 0.04271 (19)
- Third_Ventricle (14): linear fit = 1.40 x + 0.0 (72 voxels, overlap=0.054)
- Third_Ventricle (14): linear fit = 1.40 x + 0.0 (72 voxels, peak = 51), gca=50.6
- gca peak = 0.13542 (27)
- mri peak = 0.14359 ( 8)
- Fourth_Ventricle (15): linear fit = 0.25 x + 0.0 (531 voxels, overlap=0.029)
- Fourth_Ventricle (15): linear fit = 0.25 x + 0.0 (531 voxels, peak = 7), gca=6.9
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- gca peak Fourth_Ventricle = 0.13542 (27)
- gca peak CSF = 0.17123 (45)
- gca peak Left_Accumbens_area = 0.25875 (69)
- gca peak Left_undetermined = 0.96240 (36)
- gca peak Left_vessel = 0.33262 (65)
- gca peak Left_choroid_plexus = 0.09846 (46)
- gca peak Right_Inf_Lat_Vent = 0.28113 (34)
- gca peak Right_Accumbens_area = 0.27120 (72)
- gca peak Right_vessel = 0.61915 (60)
- gca peak Right_choroid_plexus = 0.12775 (51)
- gca peak Fifth_Ventricle = 0.45329 (44)
- gca peak WM_hypointensities = 0.11729 (81)
- gca peak non_WM_hypointensities = 0.10912 (56)
- gca peak Optic_Chiasm = 0.33287 (75)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.88 x + 0.0
- estimating mean wm scale to be 1.03 x + 0.0
- estimating mean csf scale to be 0.73 x + 0.0
- saving intensity scales to talairach.label_intensities.txt
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.709, neg=0, invalid=96777
- 0107: dt=129.472000, rms=0.700 (1.169%), neg=0, invalid=96777
- 0108: dt=129.472000, rms=0.697 (0.425%), neg=0, invalid=96777
- 0109: dt=110.976000, rms=0.696 (0.200%), neg=0, invalid=96777
- 0110: dt=92.480000, rms=0.695 (0.195%), neg=0, invalid=96777
- 0111: dt=110.976000, rms=0.694 (0.134%), neg=0, invalid=96777
- 0112: dt=110.976000, rms=0.693 (0.128%), neg=0, invalid=96777
- 0113: dt=110.976000, rms=0.692 (0.109%), neg=0, invalid=96777
- 0114: dt=92.480000, rms=0.691 (0.100%), neg=0, invalid=96777
- 0115: dt=129.472000, rms=0.691 (0.091%), neg=0, invalid=96777
- 0116: dt=129.472000, rms=0.690 (0.080%), neg=0, invalid=96777
- 0117: dt=110.976000, rms=0.690 (0.067%), neg=0, invalid=96777
- 0118: dt=110.976000, rms=0.689 (0.064%), neg=0, invalid=96777
- 0119: dt=92.480000, rms=0.689 (0.052%), neg=0, invalid=96777
- 0120: dt=129.472000, rms=0.688 (0.059%), neg=0, invalid=96777
- 0121: dt=110.976000, rms=0.688 (0.048%), neg=0, invalid=96777
- 0122: dt=110.976000, rms=0.688 (0.050%), neg=0, invalid=96777
- 0123: dt=110.976000, rms=0.687 (0.086%), neg=0, invalid=96777
- 0124: dt=110.976000, rms=0.686 (0.105%), neg=0, invalid=96777
- 0125: dt=110.976000, rms=0.686 (0.125%), neg=0, invalid=96777
- 0126: dt=110.976000, rms=0.685 (0.111%), neg=0, invalid=96777
- 0127: dt=110.976000, rms=0.684 (0.104%), neg=0, invalid=96777
- 0128: dt=110.976000, rms=0.683 (0.095%), neg=0, invalid=96777
- 0129: dt=110.976000, rms=0.683 (0.099%), neg=0, invalid=96777
- 0130: dt=110.976000, rms=0.682 (0.070%), neg=0, invalid=96777
- 0131: dt=110.976000, rms=0.682 (0.065%), neg=0, invalid=96777
- 0132: dt=110.976000, rms=0.681 (0.059%), neg=0, invalid=96777
- 0133: dt=110.976000, rms=0.681 (0.061%), neg=0, invalid=96777
- 0134: dt=110.976000, rms=0.681 (0.051%), neg=0, invalid=96777
- 0135: dt=110.976000, rms=0.680 (0.058%), neg=0, invalid=96777
- 0136: dt=110.976000, rms=0.680 (0.060%), neg=0, invalid=96777
- 0137: dt=110.976000, rms=0.679 (0.067%), neg=0, invalid=96777
- 0138: dt=110.976000, rms=0.679 (0.071%), neg=0, invalid=96777
- 0139: dt=110.976000, rms=0.678 (0.077%), neg=0, invalid=96777
- 0140: dt=110.976000, rms=0.678 (0.080%), neg=0, invalid=96777
- 0141: dt=110.976000, rms=0.677 (0.079%), neg=0, invalid=96777
- 0142: dt=110.976000, rms=0.677 (0.087%), neg=0, invalid=96777
- 0143: dt=110.976000, rms=0.676 (0.077%), neg=0, invalid=96777
- 0144: dt=110.976000, rms=0.676 (0.069%), neg=0, invalid=96777
- 0145: dt=110.976000, rms=0.675 (0.067%), neg=0, invalid=96777
- 0146: dt=110.976000, rms=0.675 (0.069%), neg=0, invalid=96777
- 0147: dt=110.976000, rms=0.674 (0.071%), neg=0, invalid=96777
- 0148: dt=110.976000, rms=0.674 (0.065%), neg=0, invalid=96777
- 0149: dt=110.976000, rms=0.674 (0.057%), neg=0, invalid=96777
- 0150: dt=110.976000, rms=0.673 (0.048%), neg=0, invalid=96777
- 0151: dt=110.976000, rms=0.673 (0.048%), neg=0, invalid=96777
- 0152: dt=110.976000, rms=0.673 (0.055%), neg=0, invalid=96777
- 0153: dt=110.976000, rms=0.672 (0.052%), neg=0, invalid=96777
- 0154: dt=110.976000, rms=0.672 (0.050%), neg=0, invalid=96777
- 0155: dt=110.976000, rms=0.672 (0.051%), neg=0, invalid=96777
- 0156: dt=110.976000, rms=0.671 (0.053%), neg=0, invalid=96777
- 0157: dt=110.976000, rms=0.671 (0.053%), neg=0, invalid=96777
- 0158: dt=110.976000, rms=0.671 (0.049%), neg=0, invalid=96777
- 0159: dt=110.976000, rms=0.670 (0.044%), neg=0, invalid=96777
- 0160: dt=110.976000, rms=0.670 (0.045%), neg=0, invalid=96777
- 0161: dt=110.976000, rms=0.670 (0.044%), neg=0, invalid=96777
- 0162: dt=110.976000, rms=0.669 (0.048%), neg=0, invalid=96777
- 0163: dt=110.976000, rms=0.669 (0.055%), neg=0, invalid=96777
- 0164: dt=110.976000, rms=0.669 (0.052%), neg=0, invalid=96777
- 0165: dt=110.976000, rms=0.668 (0.050%), neg=0, invalid=96777
- 0166: dt=110.976000, rms=0.668 (0.047%), neg=0, invalid=96777
- 0167: dt=110.976000, rms=0.668 (0.043%), neg=0, invalid=96777
- 0168: dt=110.976000, rms=0.667 (0.040%), neg=0, invalid=96777
- 0169: dt=110.976000, rms=0.667 (0.043%), neg=0, invalid=96777
- 0170: dt=110.976000, rms=0.667 (0.049%), neg=0, invalid=96777
- 0171: dt=110.976000, rms=0.666 (0.045%), neg=0, invalid=96777
- 0172: dt=110.976000, rms=0.666 (0.038%), neg=0, invalid=96777
- 0173: dt=110.976000, rms=0.666 (0.035%), neg=0, invalid=96777
- 0174: dt=110.976000, rms=0.666 (0.032%), neg=0, invalid=96777
- 0175: dt=110.976000, rms=0.666 (0.028%), neg=0, invalid=96777
- 0176: dt=110.976000, rms=0.665 (0.026%), neg=0, invalid=96777
- 0177: dt=110.976000, rms=0.665 (0.028%), neg=0, invalid=96777
- 0178: dt=110.976000, rms=0.665 (0.025%), neg=0, invalid=96777
- 0179: dt=110.976000, rms=0.665 (0.022%), neg=0, invalid=96777
- 0180: dt=110.976000, rms=0.665 (0.022%), neg=0, invalid=96777
- 0181: dt=1183.744000, rms=0.665 (0.021%), neg=0, invalid=96777
- 0182: dt=1183.744000, rms=0.665 (-2.593%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.665, neg=0, invalid=96777
- 0183: dt=110.976000, rms=0.664 (0.066%), neg=0, invalid=96777
- 0184: dt=129.472000, rms=0.664 (0.065%), neg=0, invalid=96777
- 0185: dt=129.472000, rms=0.664 (0.035%), neg=0, invalid=96777
- 0186: dt=129.472000, rms=0.663 (0.038%), neg=0, invalid=96777
- 0187: dt=129.472000, rms=0.663 (0.061%), neg=0, invalid=96777
- 0188: dt=129.472000, rms=0.663 (0.047%), neg=0, invalid=96777
- 0189: dt=129.472000, rms=0.662 (0.063%), neg=0, invalid=96777
- 0190: dt=129.472000, rms=0.662 (0.053%), neg=0, invalid=96777
- 0191: dt=129.472000, rms=0.661 (0.069%), neg=0, invalid=96777
- 0192: dt=129.472000, rms=0.661 (0.047%), neg=0, invalid=96777
- 0193: dt=129.472000, rms=0.661 (0.055%), neg=0, invalid=96777
- 0194: dt=129.472000, rms=0.661 (0.018%), neg=0, invalid=96777
- 0195: dt=129.472000, rms=0.660 (0.040%), neg=0, invalid=96777
- 0196: dt=129.472000, rms=0.660 (0.036%), neg=0, invalid=96777
- 0197: dt=129.472000, rms=0.660 (0.028%), neg=0, invalid=96777
- 0198: dt=129.472000, rms=0.660 (0.032%), neg=0, invalid=96777
- 0199: dt=129.472000, rms=0.659 (0.025%), neg=0, invalid=96777
- 0200: dt=129.472000, rms=0.659 (0.021%), neg=0, invalid=96777
- 0201: dt=129.472000, rms=0.659 (0.014%), neg=0, invalid=96777
- 0202: dt=32.368000, rms=0.659 (0.000%), neg=0, invalid=96777
- 0203: dt=32.368000, rms=0.659 (0.002%), neg=0, invalid=96777
- 0204: dt=32.368000, rms=0.659 (0.001%), neg=0, invalid=96777
- 0205: dt=32.368000, rms=0.659 (0.002%), neg=0, invalid=96777
- 0206: dt=32.368000, rms=0.659 (0.002%), neg=0, invalid=96777
- 0207: dt=32.368000, rms=0.659 (0.003%), neg=0, invalid=96777
- 0208: dt=32.368000, rms=0.659 (0.004%), neg=0, invalid=96777
- 0209: dt=32.368000, rms=0.659 (0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.660, neg=0, invalid=96777
- 0210: dt=62.208000, rms=0.657 (0.474%), neg=0, invalid=96777
- 0211: dt=124.416000, rms=0.653 (0.617%), neg=0, invalid=96777
- 0212: dt=36.288000, rms=0.650 (0.520%), neg=0, invalid=96777
- 0213: dt=36.288000, rms=0.648 (0.162%), neg=0, invalid=96777
- 0214: dt=145.152000, rms=0.644 (0.620%), neg=0, invalid=96777
- 0215: dt=20.736000, rms=0.643 (0.286%), neg=0, invalid=96777
- 0216: dt=580.608000, rms=0.631 (1.774%), neg=0, invalid=96777
- 0217: dt=25.920000, rms=0.629 (0.405%), neg=0, invalid=96777
- 0218: dt=36.288000, rms=0.628 (0.145%), neg=0, invalid=96777
- 0219: dt=36.288000, rms=0.627 (0.082%), neg=0, invalid=96777
- 0220: dt=103.680000, rms=0.626 (0.177%), neg=0, invalid=96777
- 0221: dt=20.736000, rms=0.625 (0.113%), neg=0, invalid=96777
- 0222: dt=414.720000, rms=0.623 (0.455%), neg=0, invalid=96777
- 0223: dt=9.072000, rms=0.621 (0.194%), neg=0, invalid=96777
- 0224: dt=2.268000, rms=0.621 (0.045%), neg=0, invalid=96777
- 0225: dt=1.134000, rms=0.621 (0.013%), neg=0, invalid=96777
- 0226: dt=0.008859, rms=0.621 (0.001%), neg=0, invalid=96777
- 0227: dt=0.004430, rms=0.621 (0.000%), neg=0, invalid=96777
- 0228: dt=0.001898, rms=0.621 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.621, neg=0, invalid=96777
- 0229: dt=0.000000, rms=0.621 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.626, neg=0, invalid=96777
- 0230: dt=0.000000, rms=0.626 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.626, neg=0, invalid=96777
- 0231: dt=0.000000, rms=0.626 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.641, neg=0, invalid=96777
- 0232: dt=2.880000, rms=0.627 (2.087%), neg=0, invalid=96777
- 0233: dt=4.032000, rms=0.612 (2.370%), neg=0, invalid=96777
- 0234: dt=4.032000, rms=0.601 (1.784%), neg=0, invalid=96777
- 0235: dt=16.128000, rms=0.571 (4.985%), neg=0, invalid=96777
- 0236: dt=4.032000, rms=0.569 (0.328%), neg=0, invalid=96777
- 0237: dt=4.032000, rms=0.568 (0.268%), neg=0, invalid=96777
- 0238: dt=4.032000, rms=0.567 (0.245%), neg=0, invalid=96777
- 0239: dt=13.824000, rms=0.562 (0.727%), neg=0, invalid=96777
- 0240: dt=4.032000, rms=0.562 (0.132%), neg=0, invalid=96777
- 0241: dt=11.520000, rms=0.560 (0.366%), neg=0, invalid=96777
- 0242: dt=2.880000, rms=0.559 (0.081%), neg=0, invalid=96777
- 0243: dt=16.128000, rms=0.557 (0.329%), neg=0, invalid=96777
- 0244: dt=4.032000, rms=0.557 (0.100%), neg=0, invalid=96777
- 0245: dt=5.846154, rms=0.556 (0.103%), neg=0, invalid=96777
- 0246: dt=3.456000, rms=0.556 (0.053%), neg=0, invalid=96777
- 0247: dt=6.545455, rms=0.555 (0.099%), neg=0, invalid=96777
- 0248: dt=4.032000, rms=0.555 (0.051%), neg=0, invalid=96777
- 0249: dt=5.000000, rms=0.555 (0.073%), neg=0, invalid=96777
- 0250: dt=4.032000, rms=0.554 (0.039%), neg=0, invalid=96777
- 0251: dt=4.032000, rms=0.554 (0.071%), neg=0, invalid=96777
- 0252: dt=4.032000, rms=0.554 (0.083%), neg=0, invalid=96777
- 0253: dt=4.032000, rms=0.553 (0.111%), neg=0, invalid=96777
- 0254: dt=4.032000, rms=0.552 (0.132%), neg=0, invalid=96777
- 0255: dt=4.032000, rms=0.551 (0.179%), neg=0, invalid=96777
- 0256: dt=4.032000, rms=0.550 (0.153%), neg=0, invalid=96777
- 0257: dt=2.016000, rms=0.550 (0.009%), neg=0, invalid=96777
- 0258: dt=2.016000, rms=0.550 (0.003%), neg=0, invalid=96777
- 0259: dt=4.032000, rms=0.550 (0.031%), neg=0, invalid=96777
- 0260: dt=9.216000, rms=0.550 (0.019%), neg=0, invalid=96777
- 0261: dt=9.216000, rms=0.550 (-0.015%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.550, neg=0, invalid=96777
- 0262: dt=4.032000, rms=0.550 (0.093%), neg=0, invalid=96777
- 0263: dt=1.894737, rms=0.549 (0.010%), neg=0, invalid=96777
- 0264: dt=1.894737, rms=0.549 (0.004%), neg=0, invalid=96777
- 0265: dt=1.894737, rms=0.549 (-0.009%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.572, neg=0, invalid=96777
- 0266: dt=0.000000, rms=0.572 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.572, neg=0, invalid=96777
- 0267: dt=0.000000, rms=0.572 (0.000%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.534, neg=0, invalid=96777
- 0268: dt=0.112000, rms=0.530 (0.899%), neg=0, invalid=96777
- 0269: dt=0.096000, rms=0.526 (0.609%), neg=0, invalid=96777
- 0270: dt=0.020000, rms=0.526 (0.107%), neg=0, invalid=96777
- 0271: dt=0.007000, rms=0.526 (0.034%), neg=0, invalid=96777
- 0272: dt=0.007000, rms=0.525 (0.037%), neg=0, invalid=96777
- 0273: dt=0.007000, rms=0.525 (0.065%), neg=0, invalid=96777
- 0274: dt=0.007000, rms=0.525 (0.093%), neg=0, invalid=96777
- 0275: dt=0.007000, rms=0.524 (0.116%), neg=0, invalid=96777
- 0276: dt=0.007000, rms=0.523 (0.137%), neg=0, invalid=96777
- 0277: dt=0.007000, rms=0.522 (0.154%), neg=0, invalid=96777
- 0278: dt=0.007000, rms=0.522 (0.165%), neg=0, invalid=96777
- 0279: dt=0.007000, rms=0.521 (0.172%), neg=0, invalid=96777
- 0280: dt=0.007000, rms=0.520 (0.178%), neg=0, invalid=96777
- 0281: dt=0.007000, rms=0.519 (0.183%), neg=0, invalid=96777
- 0282: dt=0.007000, rms=0.518 (0.184%), neg=0, invalid=96777
- 0283: dt=0.007000, rms=0.517 (0.181%), neg=0, invalid=96777
- 0284: dt=0.007000, rms=0.517 (0.018%), neg=0, invalid=96777
- 0285: dt=0.007000, rms=0.517 (0.028%), neg=0, invalid=96777
- 0286: dt=0.007000, rms=0.516 (0.041%), neg=0, invalid=96777
- 0287: dt=0.007000, rms=0.516 (0.050%), neg=0, invalid=96777
- 0288: dt=0.007000, rms=0.516 (0.062%), neg=0, invalid=96777
- 0289: dt=0.007000, rms=0.515 (0.069%), neg=0, invalid=96777
- 0290: dt=0.007000, rms=0.515 (0.075%), neg=0, invalid=96777
- 0291: dt=0.007000, rms=0.515 (0.077%), neg=0, invalid=96777
- 0292: dt=0.007000, rms=0.514 (0.080%), neg=0, invalid=96777
- 0293: dt=0.007000, rms=0.514 (0.087%), neg=0, invalid=96777
- 0294: dt=0.007000, rms=0.513 (0.086%), neg=0, invalid=96777
- 0295: dt=0.007000, rms=0.513 (0.084%), neg=0, invalid=96777
- 0296: dt=0.007000, rms=0.512 (0.087%), neg=0, invalid=96777
- 0297: dt=0.007000, rms=0.512 (0.087%), neg=0, invalid=96777
- 0298: dt=0.007000, rms=0.512 (0.084%), neg=0, invalid=96777
- 0299: dt=0.007000, rms=0.511 (0.079%), neg=0, invalid=96777
- 0300: dt=0.007000, rms=0.511 (0.077%), neg=0, invalid=96777
- 0301: dt=0.007000, rms=0.510 (0.077%), neg=0, invalid=96777
- 0302: dt=0.007000, rms=0.510 (0.072%), neg=0, invalid=96777
- 0303: dt=0.007000, rms=0.510 (0.068%), neg=0, invalid=96777
- 0304: dt=0.007000, rms=0.509 (0.065%), neg=0, invalid=96777
- 0305: dt=0.007000, rms=0.509 (0.064%), neg=0, invalid=96777
- 0306: dt=0.007000, rms=0.509 (0.058%), neg=0, invalid=96777
- 0307: dt=0.007000, rms=0.508 (0.053%), neg=0, invalid=96777
- 0308: dt=0.007000, rms=0.508 (0.049%), neg=0, invalid=96777
- 0309: dt=0.007000, rms=0.508 (0.045%), neg=0, invalid=96777
- 0310: dt=0.007000, rms=0.508 (0.044%), neg=0, invalid=96777
- 0311: dt=0.007000, rms=0.508 (0.038%), neg=0, invalid=96777
- 0312: dt=0.007000, rms=0.507 (0.035%), neg=0, invalid=96777
- 0313: dt=0.007000, rms=0.507 (0.031%), neg=0, invalid=96777
- 0314: dt=0.007000, rms=0.507 (0.032%), neg=0, invalid=96777
- 0315: dt=0.007000, rms=0.507 (0.031%), neg=0, invalid=96777
- 0316: dt=0.007000, rms=0.507 (0.025%), neg=0, invalid=96777
- 0317: dt=0.007000, rms=0.507 (0.022%), neg=0, invalid=96777
- 0318: dt=0.007000, rms=0.507 (0.021%), neg=0, invalid=96777
- 0319: dt=0.384000, rms=0.506 (0.030%), neg=0, invalid=96777
- 0320: dt=0.020000, rms=0.506 (0.007%), neg=0, invalid=96777
- 0321: dt=0.020000, rms=0.506 (0.003%), neg=0, invalid=96777
- 0322: dt=0.020000, rms=0.506 (0.005%), neg=0, invalid=96777
- 0323: dt=0.020000, rms=0.506 (0.010%), neg=0, invalid=96777
- 0324: dt=0.020000, rms=0.506 (0.013%), neg=0, invalid=96777
- 0325: dt=0.020000, rms=0.506 (0.013%), neg=0, invalid=96777
- 0326: dt=0.020000, rms=0.506 (0.016%), neg=0, invalid=96777
- 0327: dt=0.020000, rms=0.506 (0.015%), neg=0, invalid=96777
- 0328: dt=0.020000, rms=0.506 (0.021%), neg=0, invalid=96777
- 0329: dt=0.020000, rms=0.506 (0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.506, neg=0, invalid=96777
- 0330: dt=0.112000, rms=0.504 (0.305%), neg=0, invalid=96777
- 0331: dt=0.028000, rms=0.504 (0.059%), neg=0, invalid=96777
- 0332: dt=0.101190, rms=0.503 (0.197%), neg=0, invalid=96777
- 0333: dt=0.007000, rms=0.503 (0.009%), neg=0, invalid=96777
- 0334: dt=0.007000, rms=0.503 (0.011%), neg=0, invalid=96777
- 0335: dt=0.007000, rms=0.503 (0.018%), neg=0, invalid=96777
- 0336: dt=0.007000, rms=0.503 (0.030%), neg=0, invalid=96777
- 0337: dt=0.007000, rms=0.503 (0.034%), neg=0, invalid=96777
- 0338: dt=0.007000, rms=0.502 (0.043%), neg=0, invalid=96777
- 0339: dt=0.007000, rms=0.502 (0.046%), neg=0, invalid=96777
- 0340: dt=0.007000, rms=0.502 (0.048%), neg=0, invalid=96777
- 0341: dt=0.007000, rms=0.502 (0.052%), neg=0, invalid=96777
- 0342: dt=0.007000, rms=0.501 (0.054%), neg=0, invalid=96777
- 0343: dt=0.007000, rms=0.501 (0.054%), neg=0, invalid=96777
- 0344: dt=0.007000, rms=0.501 (0.053%), neg=0, invalid=96777
- 0345: dt=0.007000, rms=0.501 (0.047%), neg=0, invalid=96777
- 0346: dt=0.007000, rms=0.500 (0.048%), neg=0, invalid=96777
- 0347: dt=0.007000, rms=0.500 (0.048%), neg=0, invalid=96777
- 0348: dt=0.007000, rms=0.500 (0.048%), neg=0, invalid=96777
- 0349: dt=0.007000, rms=0.500 (0.041%), neg=0, invalid=96777
- 0350: dt=0.007000, rms=0.499 (0.041%), neg=0, invalid=96777
- 0351: dt=0.007000, rms=0.499 (0.038%), neg=0, invalid=96777
- 0352: dt=0.007000, rms=0.499 (0.034%), neg=0, invalid=96777
- 0353: dt=0.007000, rms=0.499 (0.028%), neg=0, invalid=96777
- 0354: dt=0.007000, rms=0.499 (0.025%), neg=0, invalid=96777
- 0355: dt=0.007000, rms=0.499 (0.021%), neg=0, invalid=96777
- 0356: dt=0.007000, rms=0.499 (0.020%), neg=0, invalid=96777
- 0357: dt=0.000000, rms=0.499 (0.000%), neg=0, invalid=96777
- 0358: dt=0.050000, rms=0.499 (-0.009%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ********************************
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.496, neg=0, invalid=96777
- 0359: dt=8.092000, rms=0.496 (0.001%), neg=0, invalid=96777
- 0360: dt=6.936000, rms=0.496 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.496, neg=0, invalid=96777
- 0361: dt=129.472000, rms=0.496 (0.064%), neg=0, invalid=96777
- 0362: dt=129.472000, rms=0.496 (0.030%), neg=0, invalid=96777
- 0363: dt=129.472000, rms=0.496 (0.030%), neg=0, invalid=96777
- 0364: dt=129.472000, rms=0.496 (0.031%), neg=0, invalid=96777
- 0365: dt=129.472000, rms=0.495 (0.041%), neg=0, invalid=96777
- 0366: dt=129.472000, rms=0.495 (0.049%), neg=0, invalid=96777
- 0367: dt=129.472000, rms=0.495 (0.034%), neg=0, invalid=96777
- 0368: dt=129.472000, rms=0.495 (0.035%), neg=0, invalid=96777
- 0369: dt=129.472000, rms=0.495 (0.039%), neg=0, invalid=96777
- 0370: dt=129.472000, rms=0.495 (0.030%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.495, neg=0, invalid=96777
- 0371: dt=31.104000, rms=0.494 (0.070%), neg=0, invalid=96777
- 0372: dt=31.104000, rms=0.494 (0.025%), neg=0, invalid=96777
- 0373: dt=31.104000, rms=0.494 (0.024%), neg=0, invalid=96777
- 0374: dt=31.104000, rms=0.494 (0.005%), neg=0, invalid=96777
- 0375: dt=31.104000, rms=0.494 (-0.026%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.494, neg=0, invalid=96777
- 0376: dt=62.208000, rms=0.492 (0.441%), neg=0, invalid=96777
- 0377: dt=82.944000, rms=0.491 (0.205%), neg=0, invalid=96777
- 0378: dt=82.944000, rms=0.491 (-0.114%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.491, neg=0, invalid=96777
- iter 0, gcam->neg = 12
- after 8 iterations, nbhd size=1, neg = 0
- 0379: dt=44.800000, rms=0.485 (1.123%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0380: dt=32.000000, rms=0.483 (0.449%), neg=0, invalid=96777
- 0381: dt=7.434146, rms=0.481 (0.458%), neg=0, invalid=96777
- 0382: dt=11.200000, rms=0.480 (0.216%), neg=0, invalid=96777
- 0383: dt=11.200000, rms=0.479 (0.154%), neg=0, invalid=96777
- 0384: dt=11.200000, rms=0.478 (0.258%), neg=0, invalid=96777
- 0385: dt=11.200000, rms=0.477 (0.291%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 0 iterations, nbhd size=0, neg = 0
- 0386: dt=11.200000, rms=0.475 (0.318%), neg=0, invalid=96777
- 0387: dt=11.200000, rms=0.474 (0.303%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 13 iterations, nbhd size=2, neg = 0
- 0388: dt=11.200000, rms=0.472 (0.261%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 12 iterations, nbhd size=2, neg = 0
- 0389: dt=11.200000, rms=0.471 (0.228%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0390: dt=11.200000, rms=0.470 (0.214%), neg=0, invalid=96777
- 0391: dt=11.200000, rms=0.469 (0.203%), neg=0, invalid=96777
- 0392: dt=11.200000, rms=0.468 (0.207%), neg=0, invalid=96777
- 0393: dt=11.200000, rms=0.467 (0.194%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0394: dt=11.200000, rms=0.467 (0.191%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 13 iterations, nbhd size=2, neg = 0
- 0395: dt=11.200000, rms=0.466 (0.156%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0396: dt=11.200000, rms=0.465 (0.156%), neg=0, invalid=96777
- 0397: dt=11.200000, rms=0.464 (0.161%), neg=0, invalid=96777
- 0398: dt=11.200000, rms=0.464 (0.122%), neg=0, invalid=96777
- 0399: dt=11.200000, rms=0.463 (0.122%), neg=0, invalid=96777
- 0400: dt=11.200000, rms=0.463 (0.090%), neg=0, invalid=96777
- 0401: dt=9.600000, rms=0.463 (0.020%), neg=0, invalid=96777
- 0402: dt=9.600000, rms=0.463 (0.012%), neg=0, invalid=96777
- 0403: dt=9.600000, rms=0.463 (0.016%), neg=0, invalid=96777
- 0404: dt=9.600000, rms=0.463 (0.021%), neg=0, invalid=96777
- 0405: dt=9.600000, rms=0.462 (0.020%), neg=0, invalid=96777
- 0406: dt=9.600000, rms=0.462 (0.021%), neg=0, invalid=96777
- 0407: dt=9.600000, rms=0.462 (0.011%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.462, neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 0 iterations, nbhd size=0, neg = 0
- 0408: dt=38.400000, rms=0.459 (0.629%), neg=0, invalid=96777
- 0409: dt=9.600000, rms=0.459 (0.127%), neg=0, invalid=96777
- 0410: dt=9.600000, rms=0.458 (0.102%), neg=0, invalid=96777
- 0411: dt=9.600000, rms=0.458 (0.114%), neg=0, invalid=96777
- 0412: dt=9.600000, rms=0.457 (0.130%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0413: dt=9.600000, rms=0.457 (0.103%), neg=0, invalid=96777
- 0414: dt=9.600000, rms=0.456 (0.133%), neg=0, invalid=96777
- 0415: dt=9.600000, rms=0.456 (0.070%), neg=0, invalid=96777
- 0416: dt=9.600000, rms=0.456 (0.063%), neg=0, invalid=96777
- 0417: dt=32.000000, rms=0.455 (0.039%), neg=0, invalid=96777
- 0418: dt=32.000000, rms=0.455 (-0.103%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.462, neg=0, invalid=96777
- 0419: dt=1.008000, rms=0.462 (0.010%), neg=0, invalid=96777
- 0420: dt=0.864000, rms=0.462 (0.006%), neg=0, invalid=96777
- 0421: dt=0.864000, rms=0.462 (-0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.462, neg=0, invalid=96777
- 0422: dt=4.032000, rms=0.461 (0.060%), neg=0, invalid=96777
- 0423: dt=1.008000, rms=0.461 (0.007%), neg=0, invalid=96777
- 0424: dt=1.008000, rms=0.461 (0.003%), neg=0, invalid=96777
- 0425: dt=1.008000, rms=0.461 (0.001%), neg=0, invalid=96777
- 0426: dt=1.008000, rms=0.461 (-0.014%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.471, neg=0, invalid=96777
- 0427: dt=0.064000, rms=0.471 (0.000%), neg=0, invalid=96777
- 0428: dt=0.064000, rms=0.471 (0.002%), neg=0, invalid=96777
- 0429: dt=0.016000, rms=0.471 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.471, neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 6 iterations, nbhd size=1, neg = 0
- 0430: dt=1.024000, rms=0.470 (0.126%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0431: dt=0.096000, rms=0.470 (0.004%), neg=0, invalid=96777
- 0432: dt=0.096000, rms=0.470 (0.005%), neg=0, invalid=96777
- 0433: dt=0.096000, rms=0.470 (0.010%), neg=0, invalid=96777
- 0434: dt=0.096000, rms=0.470 (0.005%), neg=0, invalid=96777
- 0435: dt=0.096000, rms=0.470 (-0.008%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.459, neg=0, invalid=96777
- iter 0, gcam->neg = 814
- after 20 iterations, nbhd size=2, neg = 0
- 0436: dt=1.813154, rms=0.419 (8.728%), neg=0, invalid=96777
- 0437: dt=0.000109, rms=0.419 (-0.003%), neg=0, invalid=96777
- 0438: dt=0.000109, rms=0.419 (0.001%), neg=0, invalid=96777
- 0439: dt=0.000109, rms=0.419 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.419, neg=0, invalid=96777
- 0440: dt=0.000312, rms=0.419 (0.000%), neg=0, invalid=96777
- 0441: dt=0.000000, rms=0.419 (-0.000%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- label assignment complete, 0 changed (0.00%)
- ***************** morphing with label term set to 0 *******************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.404, neg=0, invalid=96777
- 0442: dt=0.014450, rms=0.405 (-0.268%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- 0443: dt=32.368000, rms=0.405 (0.012%), neg=0, invalid=96777
- 0444: dt=27.744000, rms=0.405 (0.001%), neg=0, invalid=96777
- 0445: dt=27.744000, rms=0.405 (0.000%), neg=0, invalid=96777
- 0446: dt=27.744000, rms=0.405 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- 0447: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- 0448: dt=36.288000, rms=0.405 (0.043%), neg=0, invalid=96777
- 0449: dt=103.680000, rms=0.405 (0.052%), neg=0, invalid=96777
- 0450: dt=145.152000, rms=0.405 (0.037%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0451: dt=145.152000, rms=0.405 (-0.040%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.406, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0452: dt=11.200000, rms=0.405 (0.065%), neg=0, invalid=96777
- 0453: dt=2.800000, rms=0.405 (0.003%), neg=0, invalid=96777
- 0454: dt=2.800000, rms=0.405 (0.004%), neg=0, invalid=96777
- 0455: dt=2.800000, rms=0.405 (0.000%), neg=0, invalid=96777
- 0456: dt=2.800000, rms=0.405 (-0.014%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- iter 0, gcam->neg = 18
- after 24 iterations, nbhd size=3, neg = 0
- 0457: dt=32.000000, rms=0.404 (0.367%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0458: dt=19.200000, rms=0.403 (0.128%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 0 iterations, nbhd size=0, neg = 0
- 0459: dt=19.200000, rms=0.403 (0.179%), neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 28 iterations, nbhd size=3, neg = 0
- 0460: dt=19.200000, rms=0.402 (0.182%), neg=0, invalid=96777
- iter 0, gcam->neg = 43
- after 78 iterations, nbhd size=3, neg = 0
- 0461: dt=19.200000, rms=0.401 (0.094%), neg=0, invalid=96777
- iter 0, gcam->neg = 13
- after 30 iterations, nbhd size=3, neg = 0
- 0462: dt=19.200000, rms=0.401 (-0.022%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0463: dt=11.200000, rms=0.401 (0.030%), neg=0, invalid=96777
- iter 0, gcam->neg = 31
- after 28 iterations, nbhd size=2, neg = 0
- 0464: dt=44.800000, rms=0.400 (0.207%), neg=0, invalid=96777
- 0465: dt=2.800000, rms=0.400 (0.004%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.403, neg=0, invalid=96777
- iter 0, gcam->neg = 19
- after 9 iterations, nbhd size=1, neg = 0
- 0466: dt=4.571429, rms=0.403 (0.124%), neg=0, invalid=96777
- 0467: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0468: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0469: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0470: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0471: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0472: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0473: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0474: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0475: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0476: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0477: dt=0.003938, rms=0.403 (0.000%), neg=0, invalid=96777
- 0478: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0479: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0480: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0481: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0482: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0483: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0484: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0485: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0486: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0487: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0488: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0489: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0490: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0491: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0492: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0493: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0494: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0495: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0496: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0497: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0498: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0499: dt=0.003938, rms=0.403 (0.001%), neg=0, invalid=96777
- 0500: dt=0.003938, rms=0.402 (0.001%), neg=0, invalid=96777
- 0501: dt=0.003938, rms=0.402 (0.001%), neg=0, invalid=96777
- 0502: dt=0.003938, rms=0.402 (0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.402, neg=0, invalid=96777
- iter 0, gcam->neg = 125
- after 32 iterations, nbhd size=3, neg = 0
- 0503: dt=14.035088, rms=0.400 (0.502%), neg=0, invalid=96777
- 0504: dt=0.003938, rms=0.400 (0.000%), neg=0, invalid=96777
- 0505: dt=0.003938, rms=0.400 (0.000%), neg=0, invalid=96777
- 0506: dt=0.003938, rms=0.400 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.406, neg=0, invalid=96777
- 0507: dt=0.000000, rms=0.406 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.406, neg=0, invalid=96777
- 0508: dt=0.000000, rms=0.406 (0.000%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.397, neg=0, invalid=96777
- iter 0, gcam->neg = 615
- after 25 iterations, nbhd size=2, neg = 0
- 0509: dt=0.861111, rms=0.383 (3.502%), neg=0, invalid=96777
- 0510: dt=0.000078, rms=0.383 (0.003%), neg=0, invalid=96777
- 0511: dt=0.000078, rms=0.383 (0.000%), neg=0, invalid=96777
- 0512: dt=0.000078, rms=0.383 (0.000%), neg=0, invalid=96777
- 0513: dt=0.000078, rms=0.383 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.383, neg=0, invalid=96777
- 0514: dt=0.000438, rms=0.383 (0.000%), neg=0, invalid=96777
- 0515: dt=0.000438, rms=0.383 (0.000%), neg=0, invalid=96777
- 0516: dt=0.000438, rms=0.383 (-0.000%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 3 hours, 50 minutes and 55 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 16:02:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_ca_register -invert-and-save transforms/talairach.m3z
- Loading, Inverting, Saving, Exiting ...
- Reading transforms/talairach.m3z
- Inverting GCAM
- Saving inverse
- #--------------------------------------
- #@# Remove Neck Thu Aug 8 16:04:20 CEST 2013
- mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz
- erasing everything more than 25 mm from possible brain
- reading atlas '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'...
- reading input volume 'nu.mgz'...
- reading transform 'transforms/talairach.m3z'...
- removing structures at least 25 mm from brain...
- 11334035 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 34 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 16:05:54 CEST 2013
- mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- using previously computed transform transforms/talairach.lta
- reading 1 input volumes...
- logging results to talairach_with_skull_2.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu_noneck.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=13.0
- skull bounding box = (48, 20, 25) --> (201, 200, 217)
- using (99, 80, 121) as brain centroid...
- mean wm in atlas = 126, using box (80,58,97) --> (117, 102,144) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 109, scaling input intensities by 1.156
- scaling channel 0 by 1.15596
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.084 -0.025 0.027 -13.375;
- 0.037 1.224 0.174 -24.758;
- -0.043 -0.154 1.085 -3.561;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.084 -0.025 0.027 -13.375;
- 0.037 1.224 0.174 -24.758;
- -0.043 -0.154 1.085 -3.561;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.064 -0.024 0.026 -10.766;
- 0.037 1.224 0.174 -24.758;
- -0.042 -0.151 1.064 -1.506;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.064 -0.024 0.026 -10.766;
- 0.038 1.228 0.139 -21.161;
- -0.040 -0.109 1.050 -4.116;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.061 -0.024 0.026 -9.040;
- 0.038 1.229 0.148 -21.760;
- -0.041 -0.119 1.047 -3.295;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.061 -0.024 0.026 -9.040;
- 0.038 1.226 0.147 -21.425;
- -0.041 -0.119 1.047 -3.295;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 3481 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.06145 -0.02426 0.02614 -9.03973;
- 0.03777 1.22563 0.14735 -21.42546;
- -0.04076 -0.11857 1.04711 -3.29497;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.06145 -0.02426 0.02614 -9.03973;
- 0.03777 1.22563 0.14735 -21.42546;
- -0.04076 -0.11857 1.04711 -3.29497;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.061 -0.024 0.026 -9.040;
- 0.038 1.226 0.147 -21.425;
- -0.041 -0.119 1.047 -3.295;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.0)
- transform before final EM align:
- 1.061 -0.024 0.026 -9.040;
- 0.038 1.226 0.147 -21.425;
- -0.041 -0.119 1.047 -3.295;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 382743 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.06145 -0.02426 0.02614 -9.03973;
- 0.03777 1.22563 0.14735 -21.42546;
- -0.04076 -0.11857 1.04711 -3.29497;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.06145 -0.02426 0.02614 -9.03973;
- 0.03777 1.22563 0.14735 -21.42546;
- -0.04076 -0.11857 1.04711 -3.29497;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.3 tol 0.000000
- final transform:
- 1.061 -0.024 0.026 -9.040;
- 0.038 1.226 0.147 -21.425;
- -0.041 -0.119 1.047 -3.295;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 34 minutes and 8 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 16:40:03 CEST 2013
- mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
- renormalizing sequences with structure alignment, equivalent to:
- -renormalize
- -renormalize_mean 0.500
- -regularize 0.500
- reading 1 input volumes...
- reading classifier array from /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca...
- reading input volume from norm.mgz...
- average std[0] = 6.9
- reading transform from transforms/talairach.m3z...
- Atlas used for the 3D morph was /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca
- average std = 6.9 using min determinant for regularization = 4.7
- 0 singular and 0 ill-conditioned covariance matrices regularized
- labeling volume...
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.15151 (27)
- mri peak = 0.12917 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.29 x + 0.0 (249 voxels, overlap=0.006)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (249 voxels, peak = 8), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.13043 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.35 x + 0.0 (320 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (320 voxels, peak = 7), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.12444 (90)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (450 voxels, overlap=0.316)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (450 voxels, peak = 89), gca=88.8
- gca peak = 0.18160 (96)
- mri peak = 0.09677 (89)
- Left_Pallidum (13): linear fit = 0.89 x + 0.0 (309 voxels, overlap=0.221)
- Left_Pallidum (13): linear fit = 0.89 x + 0.0 (309 voxels, peak = 86), gca=85.9
- gca peak = 0.27536 (62)
- mri peak = 0.08006 (56)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (634 voxels, overlap=0.789)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (634 voxels, peak = 55), gca=54.9
- gca peak = 0.32745 (63)
- mri peak = 0.09660 (59)
- Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (657 voxels, overlap=0.604)
- Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (657 voxels, peak = 56), gca=56.4
- gca peak = 0.08597 (105)
- mri peak = 0.08969 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (40094 voxels, overlap=0.653)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (40094 voxels, peak = 108), gca=107.6
- gca peak = 0.09209 (106)
- mri peak = 0.08141 (109)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (37981 voxels, overlap=0.613)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (37981 voxels, peak = 110), gca=109.7
- gca peak = 0.07826 (63)
- mri peak = 0.05547 (51)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14279 voxels, overlap=0.375)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14279 voxels, peak = 52), gca=52.0
- gca peak = 0.08598 (64)
- mri peak = 0.05416 (49)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (14951 voxels, overlap=0.157)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (14951 voxels, peak = 51), gca=50.9
- gca peak = 0.24164 (71)
- mri peak = 0.10245 (69)
- Right_Caudate (50): linear fit = 0.95 x + 0.0 (443 voxels, overlap=1.015)
- Right_Caudate (50): linear fit = 0.95 x + 0.0 (443 voxels, peak = 68), gca=67.8
- gca peak = 0.18227 (75)
- mri peak = 0.08701 (69)
- Left_Caudate (11): linear fit = 0.87 x + 0.0 (839 voxels, overlap=0.450)
- Left_Caudate (11): linear fit = 0.87 x + 0.0 (839 voxels, peak = 65), gca=64.9
- gca peak = 0.10629 (62)
- mri peak = 0.05188 (58)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (12446 voxels, overlap=1.000)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (12446 voxels, peak = 60), gca=59.8
- gca peak = 0.11668 (59)
- mri peak = 0.05146 (55)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (12966 voxels, overlap=0.959)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (12966 voxels, peak = 55), gca=55.2
- gca peak = 0.17849 (88)
- mri peak = 0.08181 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4418 voxels, overlap=0.980)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4418 voxels, peak = 90), gca=90.2
- gca peak = 0.16819 (86)
- mri peak = 0.07725 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4104 voxels, overlap=0.998)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4104 voxels, peak = 86), gca=85.6
- gca peak = 0.41688 (64)
- mri peak = 0.09310 (63)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (294 voxels, overlap=1.032)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (294 voxels, peak = 59), gca=59.2
- gca peak = 0.42394 (62)
- mri peak = 0.06876 (65)
- Right_Amygdala (54): linear fit = 1.05 x + 0.0 (298 voxels, overlap=1.041)
- Right_Amygdala (54): linear fit = 1.05 x + 0.0 (298 voxels, peak = 65), gca=65.4
- gca peak = 0.10041 (96)
- mri peak = 0.06375 (85)
- Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (3999 voxels, overlap=0.714)
- Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (3999 voxels, peak = 89), gca=88.8
- gca peak = 0.13978 (88)
- mri peak = 0.07455 (83)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3520 voxels, overlap=0.745)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3520 voxels, peak = 82), gca=82.3
- gca peak = 0.08514 (81)
- mri peak = 0.06975 (78)
- Left_Putamen (12): linear fit = 0.94 x + 0.0 (1993 voxels, overlap=0.742)
- Left_Putamen (12): linear fit = 0.94 x + 0.0 (1993 voxels, peak = 77), gca=76.5
- gca peak = 0.09624 (82)
- mri peak = 0.08318 (79)
- Right_Putamen (51): linear fit = 0.93 x + 0.0 (1893 voxels, overlap=0.611)
- Right_Putamen (51): linear fit = 0.93 x + 0.0 (1893 voxels, peak = 76), gca=75.8
- gca peak = 0.07543 (88)
- mri peak = 0.10092 (83)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (9456 voxels, overlap=0.698)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (9456 voxels, peak = 87), gca=86.7
- gca peak = 0.12757 (95)
- mri peak = 0.06800 (92)
- Right_VentralDC (60): linear fit = 0.99 x + 0.0 (797 voxels, overlap=0.851)
- Right_VentralDC (60): linear fit = 0.99 x + 0.0 (797 voxels, peak = 94), gca=93.6
- gca peak = 0.17004 (92)
- mri peak = 0.06974 (91)
- Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1017 voxels, overlap=0.968)
- Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1017 voxels, peak = 90), gca=89.7
- gca peak = 0.21361 (36)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.26069 (23)
- mri peak = 0.11471 ( 9)
- Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (338 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (338 voxels, peak = 7), gca=7.0
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.31795 (35)
- gca peak Third_Ventricle = 0.21361 (36)
- gca peak Fourth_Ventricle = 0.26069 (23)
- gca peak CSF = 0.14367 (38)
- gca peak Left_Accumbens_area = 0.57033 (70)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.65201 (62)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.31129 (32)
- gca peak Right_Accumbens_area = 0.30219 (72)
- gca peak Right_vessel = 0.83418 (60)
- gca peak Right_choroid_plexus = 0.10189 (48)
- gca peak Fifth_Ventricle = 0.72939 (42)
- gca peak WM_hypointensities = 0.14821 (82)
- gca peak non_WM_hypointensities = 0.10354 (53)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.90 x + 0.0
- estimating mean wm scale to be 1.03 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.31600 (11)
- mri peak = 0.12917 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (249 voxels, overlap=0.969)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (249 voxels, peak = 8), gca=7.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.13043 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (320 voxels, overlap=0.968)
- Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (320 voxels, peak = 8), gca=8.1
- gca peak = 0.32314 (89)
- mri peak = 0.12444 (90)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (450 voxels, overlap=1.013)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (450 voxels, peak = 89), gca=89.4
- gca peak = 0.18431 (86)
- mri peak = 0.09677 (89)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (309 voxels, overlap=1.004)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (309 voxels, peak = 86), gca=85.6
- gca peak = 0.30149 (55)
- mri peak = 0.08006 (56)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (634 voxels, overlap=1.007)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (634 voxels, peak = 55), gca=55.0
- gca peak = 0.26751 (56)
- mri peak = 0.09660 (59)
- Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (657 voxels, overlap=1.005)
- Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (657 voxels, peak = 57), gca=57.4
- gca peak = 0.08344 (108)
- mri peak = 0.08969 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40094 voxels, overlap=0.757)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40094 voxels, peak = 108), gca=108.0
- gca peak = 0.08545 (110)
- mri peak = 0.08141 (109)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37981 voxels, overlap=0.744)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37981 voxels, peak = 110), gca=110.0
- gca peak = 0.09526 (52)
- mri peak = 0.05547 (51)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (14279 voxels, overlap=0.995)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (14279 voxels, peak = 52), gca=52.0
- gca peak = 0.11029 (51)
- mri peak = 0.05416 (49)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14951 voxels, overlap=0.995)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14951 voxels, peak = 50), gca=50.2
- gca peak = 0.26963 (70)
- mri peak = 0.10245 (69)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (443 voxels, overlap=1.009)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (443 voxels, peak = 70), gca=70.0
- gca peak = 0.16578 (65)
- mri peak = 0.08701 (69)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (839 voxels, overlap=0.997)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (839 voxels, peak = 65), gca=65.0
- gca peak = 0.10995 (60)
- mri peak = 0.05188 (58)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (12446 voxels, overlap=0.997)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (12446 voxels, peak = 62), gca=61.5
- gca peak = 0.12960 (56)
- mri peak = 0.05146 (55)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (12966 voxels, overlap=0.999)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (12966 voxels, peak = 57), gca=57.4
- gca peak = 0.16635 (89)
- mri peak = 0.08181 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4418 voxels, overlap=0.995)
- Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4418 voxels, peak = 88), gca=87.7
- gca peak = 0.17240 (86)
- mri peak = 0.07725 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4104 voxels, overlap=0.997)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4104 voxels, peak = 87), gca=87.3
- gca peak = 0.41681 (59)
- mri peak = 0.09310 (63)
- Left_Amygdala (18): linear fit = 1.02 x + 0.0 (294 voxels, overlap=1.027)
- Left_Amygdala (18): linear fit = 1.02 x + 0.0 (294 voxels, peak = 60), gca=60.5
- gca peak = 0.36793 (66)
- mri peak = 0.06876 (65)
- Right_Amygdala (54): linear fit = 0.99 x + 0.0 (298 voxels, overlap=1.009)
- Right_Amygdala (54): linear fit = 0.99 x + 0.0 (298 voxels, peak = 65), gca=65.0
- gca peak = 0.11808 (89)
- mri peak = 0.06375 (85)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3999 voxels, overlap=0.985)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3999 voxels, peak = 90), gca=90.3
- gca peak = 0.13307 (82)
- mri peak = 0.07455 (83)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3520 voxels, overlap=0.996)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3520 voxels, peak = 82), gca=81.6
- gca peak = 0.09242 (76)
- mri peak = 0.06975 (78)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (1993 voxels, overlap=0.999)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (1993 voxels, peak = 75), gca=74.9
- gca peak = 0.12028 (70)
- mri peak = 0.08318 (79)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1893 voxels, overlap=0.989)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1893 voxels, peak = 70), gca=70.0
- gca peak = 0.07619 (81)
- mri peak = 0.10092 (83)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (9456 voxels, overlap=0.721)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (9456 voxels, peak = 81), gca=80.6
- gca peak = 0.13695 (93)
- mri peak = 0.06800 (92)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (797 voxels, overlap=0.837)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (797 voxels, peak = 93), gca=92.5
- gca peak = 0.15932 (90)
- mri peak = 0.06974 (91)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1017 voxels, overlap=0.943)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1017 voxels, peak = 90), gca=89.6
- gca peak = 0.35640 (14)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.33827 ( 9)
- mri peak = 0.11471 ( 9)
- Fourth_Ventricle (15): linear fit = 1.17 x + 0.0 (338 voxels, overlap=0.959)
- Fourth_Ventricle (15): linear fit = 1.17 x + 0.0 (338 voxels, peak = 11), gca=10.6
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.23697 (32)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.44858 (60)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.42706 (62)
- gca peak Left_choroid_plexus = 0.09164 (48)
- gca peak Right_Inf_Lat_Vent = 0.33369 (28)
- gca peak Right_Accumbens_area = 0.30143 (69)
- gca peak Right_vessel = 0.53048 (60)
- gca peak Right_choroid_plexus = 0.10321 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17627 (84)
- gca peak non_WM_hypointensities = 0.08625 (54)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.93 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
- 10951 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels)
- 267 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 83596 changed. image ll: -2.175, PF=1.000
- pass 2: 15188 changed. image ll: -2.172, PF=1.000
- pass 3: 5682 changed.
- pass 4: 2557 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 21 minutes and 21 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/cc_up.lta sub004
- will read input aseg from aseg.auto_noCCseg.mgz
- writing aseg with cc labels to aseg.auto.mgz
- will write lta as /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/norm.mgz
- 26307 voxels in left wm, 26391 in right wm, xrange [123, 131]
- searching rotation angles z=[-4 10], y=[-6 8]
-
searching scale 1 Z rot -4.4
searching scale 1 Z rot -4.2
searching scale 1 Z rot -3.9
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.4
searching scale 1 Z rot -3.2
searching scale 1 Z rot -2.9
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.4
searching scale 1 Z rot -2.2
searching scale 1 Z rot -1.9
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.4
searching scale 1 Z rot -1.2
searching scale 1 Z rot -0.9
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.4
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.1
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.6
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.1
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.6
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.1
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.6
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.1
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.6
searching scale 1 Z rot 3.8
searching scale 1 Z rot 4.1
searching scale 1 Z rot 4.3
searching scale 1 Z rot 4.6
searching scale 1 Z rot 4.8
searching scale 1 Z rot 5.1
searching scale 1 Z rot 5.3
searching scale 1 Z rot 5.6
searching scale 1 Z rot 5.8
searching scale 1 Z rot 6.1
searching scale 1 Z rot 6.3
searching scale 1 Z rot 6.6
searching scale 1 Z rot 6.8
searching scale 1 Z rot 7.1
searching scale 1 Z rot 7.3
searching scale 1 Z rot 7.6
searching scale 1 Z rot 7.8
searching scale 1 Z rot 8.1
searching scale 1 Z rot 8.3
searching scale 1 Z rot 8.6
searching scale 1 Z rot 8.8
searching scale 1 Z rot 9.1
searching scale 1 Z rot 9.3 global minimum found at slice 126.4, rotations (1.31, 2.59)
- final transformation (x=126.4, yr=1.314, zr=2.592):
- 0.999 -0.045 0.023 2.449;
- 0.045 0.999 0.001 44.235;
- -0.023 0.000 1.000 8.931;
- 0.000 0.000 0.000 1.000;
- updating x range to be [126, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 148 108
- eigenvectors:
- 0.000 -0.000 1.000;
- -0.024 -1.000 -0.000;
- 1.000 -0.024 -0.000;
- error in mid anterior detected - correcting...
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 0.8 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 17:02:10 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 17:02:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
- using segmentation for initial intensity normalization
- using MR volume brainmask.mgz to mask input volume...
- reading from norm.mgz...
- Reading aseg aseg.mgz
- normalizing image...
- processing with aseg
- removing outliers in the aseg WM...
- 2658 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 30 (30)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 57 (57), valley at 31 (31)
- csf peak at 28, setting threshold to 47
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 22 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 17:06:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1520890 voxels in mask (pct= 9.07)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 17:06:37 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (107.0): 107.1 +- 4.8 [80.0 --> 125.0]
- GM (67.0) : 66.6 +- 9.6 [30.0 --> 96.0]
- setting bottom of white matter range to 76.3
- setting top of gray matter range to 85.9
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- using local geometry to label remaining ambiguous voxels...
- reclassifying voxels using Gaussian border classifier...
- removing voxels with positive offset direction...
- smoothing T1 volume with sigma = 0.250
- removing 1-dimensional structures...
- 6872 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 4842 filled
- 268 bright non-wm voxels segmented.
- 3738 diagonally connected voxels added...
- white matter segmentation took 1.8 minutes
- writing output to wm.seg.mgz...
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.69 minutes
- reading wm segmentation from wm.seg.mgz...
- 54 voxels added to wm to prevent paths from MTL structures to cortex
- 951 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 34614 voxels turned on, 41414 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 0 new 0
- 115,126,128 old 0 new 0
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 12 found - 12 modified | TOTAL: 12
- pass 2 (xy+): 0 found - 12 modified | TOTAL: 12
- pass 1 (xy-): 16 found - 16 modified | TOTAL: 28
- pass 2 (xy-): 0 found - 16 modified | TOTAL: 28
- pass 1 (yz+): 13 found - 13 modified | TOTAL: 41
- pass 2 (yz+): 0 found - 13 modified | TOTAL: 41
- pass 1 (yz-): 21 found - 21 modified | TOTAL: 62
- pass 2 (yz-): 0 found - 21 modified | TOTAL: 62
- pass 1 (xz+): 14 found - 14 modified | TOTAL: 76
- pass 2 (xz+): 0 found - 14 modified | TOTAL: 76
- pass 1 (xz-): 19 found - 19 modified | TOTAL: 95
- pass 2 (xz-): 0 found - 19 modified | TOTAL: 95
- Iteration Number : 1
- pass 1 (+++): 4 found - 4 modified | TOTAL: 4
- pass 2 (+++): 0 found - 4 modified | TOTAL: 4
- pass 1 (+++): 16 found - 16 modified | TOTAL: 20
- pass 2 (+++): 0 found - 16 modified | TOTAL: 20
- pass 1 (+++): 18 found - 18 modified | TOTAL: 38
- pass 2 (+++): 0 found - 18 modified | TOTAL: 38
- pass 1 (+++): 10 found - 10 modified | TOTAL: 48
- pass 2 (+++): 0 found - 10 modified | TOTAL: 48
- Iteration Number : 1
- pass 1 (++): 135 found - 135 modified | TOTAL: 135
- pass 2 (++): 0 found - 135 modified | TOTAL: 135
- pass 1 (+-): 92 found - 92 modified | TOTAL: 227
- pass 2 (+-): 0 found - 92 modified | TOTAL: 227
- pass 1 (--): 92 found - 92 modified | TOTAL: 319
- pass 2 (--): 0 found - 92 modified | TOTAL: 319
- pass 1 (-+): 107 found - 107 modified | TOTAL: 426
- pass 2 (-+): 0 found - 107 modified | TOTAL: 426
- Iteration Number : 2
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 4 found - 4 modified | TOTAL: 7
- pass 2 (xy-): 0 found - 4 modified | TOTAL: 7
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 9
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 9
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 11
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 11
- pass 1 (xz+): 3 found - 3 modified | TOTAL: 14
- pass 2 (xz+): 0 found - 3 modified | TOTAL: 14
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 17
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 17
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 3 found - 3 modified | TOTAL: 4
- pass 2 (+-): 0 found - 3 modified | TOTAL: 4
- pass 1 (--): 1 found - 1 modified | TOTAL: 5
- pass 2 (--): 0 found - 1 modified | TOTAL: 5
- pass 1 (-+): 0 found - 0 modified | TOTAL: 5
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 591 (out of 529868: 0.111537)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 17:09:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
- logging cutting plane coordinates to ../scripts/ponscc.cut.log...
- INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
- using segmentation aseg.auto_noCCseg.mgz...
- reading input volume...done.
- searching for cutting planes...voxel to talairach voxel transform
- 1.084 -0.025 0.027 -13.375;
- 0.034 1.138 0.162 -14.581;
- -0.040 -0.143 1.009 4.085;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.084 -0.025 0.027 -13.375;
- 0.034 1.138 0.162 -14.581;
- -0.040 -0.143 1.009 4.085;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1217 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75)
- no need to search
- using seed (125, 110, 91), TAL = (3.0, -37.0, 18.0)
- talairach voxel to voxel transform
- 0.921 0.017 -0.027 12.668;
- -0.032 0.861 -0.137 12.676;
- 0.032 0.123 0.970 -1.746;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (125, 110, 91) --> (3.0, -37.0, 18.0)
- done.
- writing output to filled.mgz...
- filling took 1.0 minutes
- talairach cc position changed to (3.00, -37.00, 18.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(21.00, -37.00, 18.00) SRC: (110.56, 91.42, 103.50)
- search lh wm seed point around talairach space (-15.00, -37.00, 18.00), SRC: (143.71, 90.25, 104.66)
- compute mri_fill using aseg
- Erasing Brain Stem and Cerebellum ...
- Define left and right masks using aseg:
- Building Voronoi diagram ...
- Using the Voronoi diagram to separate WM into two hemispheres ...
- Find the largest connected component for each hemisphere ...
- #--------------------------------------------
- #@# Tessellate lh Thu Aug 8 17:10:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 2 found - 2 modified | TOTAL: 5
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 5
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 5
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 5
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 7
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 7
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 7
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 3 found - 3 modified | TOTAL: 3
- pass 2 (--): 0 found - 3 modified | TOTAL: 3
- pass 1 (-+): 0 found - 0 modified | TOTAL: 3
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 10 (out of 252044: 0.003968)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 40: 21 vertices, 30 faces
- slice 50: 3499 vertices, 3691 faces
- slice 60: 10235 vertices, 10512 faces
- slice 70: 18815 vertices, 19113 faces
- slice 80: 28618 vertices, 29002 faces
- slice 90: 39144 vertices, 39515 faces
- slice 100: 49871 vertices, 50217 faces
- slice 110: 61245 vertices, 61640 faces
- slice 120: 72468 vertices, 72858 faces
- slice 130: 83557 vertices, 83951 faces
- slice 140: 93735 vertices, 94096 faces
- slice 150: 104161 vertices, 104520 faces
- slice 160: 112283 vertices, 112550 faces
- slice 170: 119192 vertices, 119452 faces
- slice 180: 125750 vertices, 125986 faces
- slice 190: 131713 vertices, 131918 faces
- slice 200: 135588 vertices, 135708 faces
- slice 210: 136088 vertices, 136112 faces
- slice 220: 136088 vertices, 136112 faces
- slice 230: 136088 vertices, 136112 faces
- slice 240: 136088 vertices, 136112 faces
- slice 250: 136088 vertices, 136112 faces
- using the conformed surface RAS to save vertex points...
- writing ../surf/lh.orig.nofix
- using vox2ras matrix:
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- rm -f ../mri/filled-pretess255.mgz
- mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
- counting number of connected components...
- 136088 voxel in cpt #1: X=-24 [v=136088,e=408336,f=272224] located at (-26.335114, -11.415216, 38.139431)
- For the whole surface: X=-24 [v=136088,e=408336,f=272224]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 17:10:22 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 lh Thu Aug 8 17:10:26 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- avg radius = 46.6 mm, total surface area = 71807 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.099 (target=0.015)
step 005: RMS=0.072 (target=0.015)
step 010: RMS=0.052 (target=0.015)
step 015: RMS=0.043 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.033 (target=0.015)
step 030: RMS=0.029 (target=0.015)
step 035: RMS=0.026 (target=0.015)
step 040: RMS=0.025 (target=0.015)
step 045: RMS=0.024 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.022 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 17:11:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.98 +- 0.58 (0.00-->6.97) (max @ vno 100899 --> 100926)
- face area 0.02 +- 0.03 (-0.04-->0.54)
- scaling brain by 0.304...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=177.127, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.867, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.308, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.573, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.737, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.843, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.918, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.977, avgs=0
- 040/300: dt: 0.9000, rms radial error=171.028, avgs=0
- 045/300: dt: 0.9000, rms radial error=170.077, avgs=0
- 050/300: dt: 0.9000, rms radial error=169.127, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.179, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.235, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.295, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.360, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.430, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.504, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.583, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.667, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.757, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.852, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.951, avgs=0
- 110/300: dt: 0.9000, rms radial error=158.056, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.166, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.280, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.400, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.524, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.653, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.786, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.925, avgs=0
- 150/300: dt: 0.9000, rms radial error=151.068, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.216, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.369, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.526, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.689, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.855, avgs=0
- 180/300: dt: 0.9000, rms radial error=146.027, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.203, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.384, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.569, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.759, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.954, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.153, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.357, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.566, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.779, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.996, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.218, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.444, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.675, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.910, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.149, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.392, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.639, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.891, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.147, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.407, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.672, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.940, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.213, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.489, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 16045.74
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
- epoch 2 (K=40.0), pass 1, starting sse = 2726.62
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00006
- epoch 3 (K=160.0), pass 1, starting sse = 286.83
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.12/12 = 0.00969
- epoch 4 (K=640.0), pass 1, starting sse = 15.24
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.27/21 = 0.01288
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.11 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 17:17:29 CEST 2013
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub004 lh
- reading spherical homeomorphism from 'qsphere.nofix'
- using genetic algorithm with optimized parameters
- setting seed for random number genererator to 1234
- *************************************************************
- Topology Correction Parameters
- retessellation mode: genetic search
- number of patches/generation : 10
- number of generations : 10
- surface mri loglikelihood coefficient : 1.0
- volume mri loglikelihood coefficient : 10.0
- normal dot loglikelihood coefficient : 1.0
- quadratic curvature loglikelihood coefficient : 1.0
- volume resolution : 2
- eliminate vertices during search : 1
- initial patch selection : 1
- select all defect vertices : 0
- ordering dependant retessellation: 0
- use precomputed edge table : 0
- smooth retessellated patch : 2
- match retessellated patch : 1
- verbose mode : 0
- *************************************************************
- INFO: assuming .mgz format
- $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- before topology correction, eno=-24 (nv=136088, nf=272224, ne=408336, g=13)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 1954 ambiguous faces found in tessellation
- segmenting defects...
- 17 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 8 into 7
- -merging segment 15 into 14
- 15 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7671 (-4.8835)
- -vertex loglikelihood: -6.6171 (-3.3085)
- -normal dot loglikelihood: -3.5922 (-3.5922)
- -quad curv loglikelihood: -6.4288 (-3.2144)
- Total Loglikelihood : -26.4051
- CORRECTING DEFECT 0 (vertices=17, convex hull=31)
- After retessellation of defect 0, euler #=-13 (134920,404373,269440) : difference with theory (-12) = 1
- CORRECTING DEFECT 1 (vertices=90, convex hull=64)
- After retessellation of defect 1, euler #=-12 (134935,404449,269502) : difference with theory (-11) = 1
- CORRECTING DEFECT 2 (vertices=29, convex hull=34)
- After retessellation of defect 2, euler #=-11 (134946,404493,269536) : difference with theory (-10) = 1
- CORRECTING DEFECT 3 (vertices=31, convex hull=54)
- After retessellation of defect 3, euler #=-10 (134957,404547,269580) : difference with theory (-9) = 1
- CORRECTING DEFECT 4 (vertices=286, convex hull=95)
- After retessellation of defect 4, euler #=-9 (134993,404702,269700) : difference with theory (-8) = 1
- CORRECTING DEFECT 5 (vertices=70, convex hull=65)
- After retessellation of defect 5, euler #=-8 (135010,404783,269765) : difference with theory (-7) = 1
- CORRECTING DEFECT 6 (vertices=58, convex hull=45)
- After retessellation of defect 6, euler #=-7 (135029,404859,269823) : difference with theory (-6) = 1
- CORRECTING DEFECT 7 (vertices=89, convex hull=110)
- After retessellation of defect 7, euler #=-5 (135059,404997,269933) : difference with theory (-5) = 0
- CORRECTING DEFECT 8 (vertices=41, convex hull=30)
- After retessellation of defect 8, euler #=-4 (135063,405018,269951) : difference with theory (-4) = 0
- CORRECTING DEFECT 9 (vertices=8, convex hull=18)
- After retessellation of defect 9, euler #=-3 (135065,405029,269961) : difference with theory (-3) = 0
- CORRECTING DEFECT 10 (vertices=98, convex hull=55)
- Warning - incorrect dp selected!!!!(-123.989406 >= -123.989407 )
- After retessellation of defect 10, euler #=-2 (135070,405067,269995) : difference with theory (-2) = 0
- CORRECTING DEFECT 11 (vertices=178, convex hull=52)
- After retessellation of defect 11, euler #=-1 (135092,405152,270059) : difference with theory (-1) = 0
- CORRECTING DEFECT 12 (vertices=46, convex hull=67)
- After retessellation of defect 12, euler #=0 (135116,405254,270138) : difference with theory (0) = 0
- CORRECTING DEFECT 13 (vertices=107, convex hull=135)
- After retessellation of defect 13, euler #=1 (135151,405427,270277) : difference with theory (1) = 0
- CORRECTING DEFECT 14 (vertices=22, convex hull=53)
- After retessellation of defect 14, euler #=2 (135159,405471,270314) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.10-->5.73) (max @ vno 127858 --> 130559)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.21 (0.10-->5.73) (max @ vno 127858 --> 130559)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 63 mutations (36.0%), 112 crossovers (64.0%), 24 vertices were eliminated
- building final representation...
- 929 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=135159, nf=270314, ne=405471, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 11.9 minutes
- 0 defective edges
- removing intersecting faces
- 000: 81 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 135159 - 405471 + 270314 = 2 --> 0 holes
- F =2V-4: 270314 = 270318-4 (0)
- 2E=3F: 810942 = 810942 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 11 intersecting
- 001: 2 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 17:29:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub004 lh
- only generating white matter surface
- not using aparc to prevent surfaces crossing the midline
- INFO: assuming MGZ format for volumes.
- using brain.finalsurfs as T1 volume...
- $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- 16986 bright wm thresholded.
- 439 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.orig...
- computing class statistics...
- border white: 249466 voxels (1.49%)
- border gray 280050 voxels (1.67%)
- WM (92.0): 93.6 +- 10.0 [70.0 --> 110.0]
- GM (76.0) : 73.8 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.1 (was 70)
- setting MAX_BORDER_WHITE to 115.0 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.1 (was 40)
- setting MAX_GRAY to 95.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.2 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.02-->3.80) (max @ vno 131023 --> 135148)
- face area 0.28 +- 0.12 (0.00-->2.46)
- mean absolute distance = 0.63 +- 0.74
- 3756 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 93.4, mean outside = 69.0
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=73.5, 76 (76) missing vertices, mean dist 0.3 [0.5 (%32.2)->0.7 (%67.8))]
- %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.25 (0.07-->3.96) (max @ vno 85959 --> 84931)
- face area 0.28 +- 0.13 (0.00-->2.07)
- mean absolute distance = 0.30 +- 0.43
- 2516 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7107429.5, rms=13.49
- 001: dt: 0.5000, sse=6942656.5, rms=9.651 (0.000%)
- 002: dt: 0.5000, sse=7135381.0, rms=7.411 (0.000%)
- 003: dt: 0.5000, sse=7289946.0, rms=6.014 (0.000%)
- 004: dt: 0.5000, sse=7513136.5, rms=5.225 (0.000%)
- 005: dt: 0.5000, sse=7585499.5, rms=4.817 (0.000%)
- 006: dt: 0.5000, sse=7708704.5, rms=4.619 (0.000%)
- 007: dt: 0.5000, sse=7643470.5, rms=4.511 (0.000%)
- 008: dt: 0.5000, sse=7711329.0, rms=4.435 (0.000%)
- rms = 4.40, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=7609633.0, rms=4.396 (0.000%)
- 010: dt: 0.2500, sse=4760675.0, rms=2.988 (0.000%)
- 011: dt: 0.2500, sse=4304448.5, rms=2.512 (0.000%)
- 012: dt: 0.2500, sse=4057777.0, rms=2.402 (0.000%)
- 013: dt: 0.2500, sse=3973015.0, rms=2.312 (0.000%)
- rms = 2.27, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=3885342.2, rms=2.274 (0.000%)
- 015: dt: 0.1250, sse=3648467.8, rms=1.994 (0.000%)
- rms = 1.96, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=3607500.2, rms=1.956 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=78.3, 56 (28) missing vertices, mean dist -0.2 [0.3 (%80.3)->0.2 (%19.7))]
- %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.05-->4.06) (max @ vno 85959 --> 84931)
- face area 0.35 +- 0.16 (0.00-->2.74)
- mean absolute distance = 0.20 +- 0.29
- 2963 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4650178.0, rms=6.33
- 017: dt: 0.5000, sse=4758465.0, rms=4.253 (0.000%)
- rms = 4.52, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4303291.0, rms=3.085 (0.000%)
- 019: dt: 0.2500, sse=4118646.2, rms=2.390 (0.000%)
- 020: dt: 0.2500, sse=4056205.5, rms=1.918 (0.000%)
- 021: dt: 0.2500, sse=4030144.5, rms=1.828 (0.000%)
- 022: dt: 0.2500, sse=3972718.0, rms=1.722 (0.000%)
- rms = 1.74, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.1250, sse=3921632.2, rms=1.639 (0.000%)
- 024: dt: 0.1250, sse=3849120.8, rms=1.526 (0.000%)
- rms = 1.52, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=3814530.2, rms=1.519 (0.000%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=81.3, 49 (22) missing vertices, mean dist -0.1 [0.2 (%75.7)->0.2 (%24.3))]
- %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.11-->4.10) (max @ vno 85959 --> 84931)
- face area 0.34 +- 0.16 (0.00-->2.91)
- mean absolute distance = 0.16 +- 0.23
- 3135 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4118448.2, rms=3.91
- rms = 4.11, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=3953156.2, rms=2.695 (0.000%)
- 027: dt: 0.2500, sse=3898638.0, rms=1.734 (0.000%)
- 028: dt: 0.2500, sse=3920736.0, rms=1.557 (0.000%)
- 029: dt: 0.2500, sse=3958466.2, rms=1.482 (0.000%)
- rms = 1.53, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=3914349.2, rms=1.417 (0.000%)
- 031: dt: 0.1250, sse=3849214.2, rms=1.342 (0.000%)
- rms = 1.34, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3849214.2, rms=1.342 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=82.2, 56 (22) missing vertices, mean dist -0.0 [0.2 (%57.5)->0.1 (%42.5))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=3872071.2, rms=1.72
- rms = 2.62, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=3932723.2, rms=1.154 (0.000%)
- 034: dt: 0.2500, sse=4071440.5, rms=1.003 (0.000%)
- rms = 1.01, time step reduction 2 of 3 to 0.125...
- rms = 0.99, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4071538.2, rms=0.993 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 14 non-cortical segments detected
- only using segment with 1914 vertices
- erasing segment 1 (vno[0] = 58587)
- erasing segment 2 (vno[0] = 59709)
- erasing segment 3 (vno[0] = 82772)
- erasing segment 4 (vno[0] = 93734)
- erasing segment 5 (vno[0] = 95862)
- erasing segment 6 (vno[0] = 97922)
- erasing segment 7 (vno[0] = 99165)
- erasing segment 8 (vno[0] = 100109)
- erasing segment 9 (vno[0] = 103841)
- erasing segment 10 (vno[0] = 103889)
- erasing segment 11 (vno[0] = 104622)
- erasing segment 12 (vno[0] = 106348)
- erasing segment 13 (vno[0] = 107770)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.area
- vertex spacing 0.89 +- 0.25 (0.03-->4.18) (max @ vno 84931 --> 85959)
- face area 0.33 +- 0.15 (0.00-->3.02)
- refinement took 7.2 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 17:36:42 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 lh Thu Aug 8 17:36:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 46.8 mm, total surface area = 82388 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.114 (target=0.015)
step 005: RMS=0.079 (target=0.015)
step 010: RMS=0.056 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.038 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.026 (target=0.015)
step 035: RMS=0.022 (target=0.015)
step 040: RMS=0.019 (target=0.015)
step 045: RMS=0.017 (target=0.015)
step 050: RMS=0.016 (target=0.015)
- inflation complete.
- inflation took 0.5 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 175 vertices thresholded to be in k1 ~ [-0.20 1.22], k2 ~ [-0.09 0.05]
- total integrated curvature = 0.614*4pi (7.717) --> 0 handles
- ICI = 1.7, FI = 10.3, variation=178.038
- 94 vertices thresholded to be in [-0.02 0.01]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 97 vertices thresholded to be in [-0.13 0.23]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 17:39:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub004 lh curv sulc
- Toggling save flag on curvature files [ ok ]
- Outputting results using filestem [ ../stats/lh.curv.stats ]
- Toggling save flag on curvature files [ ok ]
- Setting surface [ sub004/lh.smoothwm ]
- Reading surface... [ ok ]
- Setting texture [ curv ]
- Reading texture... [ ok ]
- Setting texture [ sulc ]
- Reading texture...Gb_filter = 0
- [ ok ]
- Calculating Discrete Principal Curvatures...
- Determining geometric order for vertex faces... [####################] [ ok ]
- Determining KH curvatures... [####################] [ ok ]
- Determining k1k2 curvatures... [####################] [ ok ]
- deltaViolations [ 241 ]
- Gb_filter = 0
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 17:39:09 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- scaling brain by 0.283...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %21.00
- pass 1: epoch 2 of 3 starting distance error %20.95
- unfolding complete - removing small folds...
- starting distance error %20.90
- removing remaining folds...
- final distance error %20.92
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.82 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 18:28:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_register -curv ../surf/lh.sphere /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg
- using smoothwm curvature for final alignment
- $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading surface from ../surf/lh.sphere...
- reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
- MRISregister() -------
- max_passes = 4
- min_degrees = 0.500000
- max_degrees = 64.000000
- nangles = 8
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height -1.000000
- momentum 0.950000
- nbhd_size -10
- max_nbrs 10
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 16 (10)
- use curv 16
- no sulc 0
- no rigid align 0
- mris->nsize 1
- mris->hemisphere 0
- randomSeed 0
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
- using quadratic fit line minimization
- --------------------
- 1 Reading lh.sulc
- curvature mean = 0.000, std = 0.571
- curvature mean = 0.017, std = 0.931
- curvature mean = 0.022, std = 0.850
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (0.00, -8.00, 0.00) sse = 286993.7, tmin=2.2067
- d=16.00 min @ (0.00, 4.00, 0.00) sse = 273883.2, tmin=3.3249
- d=8.00 min @ (2.00, 0.00, 2.00) sse = 270777.6, tmin=4.4523
- d=4.00 min @ (-1.00, 0.00, -1.00) sse = 270772.4, tmin=5.5843
- d=2.00 min @ (0.50, 0.50, 0.50) sse = 270343.5, tmin=6.7711
- d=1.00 min @ (0.00, -0.25, -0.25) sse = 270294.5, tmin=7.9431
- d=0.50 min @ (0.00, 0.12, 0.12) sse = 270284.8, tmin=9.1114
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 9.11 min
- curvature mean = -0.000, std = 0.945
- curvature mean = 0.011, std = 0.935
- curvature mean = -0.001, std = 0.958
- curvature mean = 0.005, std = 0.971
- curvature mean = -0.002, std = 0.959
- curvature mean = 0.001, std = 0.987
- 2 Reading smoothwm
- curvature mean = -0.021, std = 0.289
- curvature mean = 0.003, std = 0.067
- curvature mean = 0.064, std = 0.342
- curvature mean = 0.003, std = 0.079
- curvature mean = 0.026, std = 0.538
- curvature mean = 0.004, std = 0.084
- curvature mean = 0.013, std = 0.680
- curvature mean = 0.004, std = 0.087
- curvature mean = 0.004, std = 0.788
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 18:56:59 CEST 2013
- mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- reading surface from ../surf/lh.white...
- writing curvature file ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv lh Thu Aug 8 18:57:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/lh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/lh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc lh Thu Aug 8 18:57:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub004 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
- reading color table from GCSA file....
- average std = 1.0 using min determinant for regularization = 0.011
- 0 singular and 384 ill-conditioned covariance matrices regularized
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 1091 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3027 changed, 135159 examined...
- 001: 688 changed, 12939 examined...
- 002: 163 changed, 3752 examined...
- 003: 38 changed, 974 examined...
- 004: 13 changed, 241 examined...
- 005: 5 changed, 81 examined...
- 006: 1 changed, 29 examined...
- 007: 0 changed, 9 examined...
- 198 labels changed using aseg
- 000: 118 total segments, 75 labels (272 vertices) changed
- 001: 45 total segments, 2 labels (4 vertices) changed
- 002: 43 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 40 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1432 vertices marked for relabeling...
- 1432 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 2 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 18:58:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub004 lh
- -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
- INFO: assuming MGZ format for volumes.
- using brain.finalsurfs as T1 volume...
- $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- 16986 bright wm thresholded.
- 439 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.orig...
- computing class statistics...
- border white: 249466 voxels (1.49%)
- border gray 280050 voxels (1.67%)
- WM (92.0): 93.6 +- 10.0 [70.0 --> 110.0]
- GM (76.0) : 73.8 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.1 (was 70)
- setting MAX_BORDER_WHITE to 115.0 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.1 (was 40)
- setting MAX_GRAY to 95.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.2 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 93.4, mean outside = 69.0
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.02-->3.80) (max @ vno 131023 --> 135148)
- face area 0.28 +- 0.12 (0.00-->2.46)
- mean absolute distance = 0.63 +- 0.75
- 3793 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 58 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 4 with 10 points - only 0.00% unknown
- deleting segment 5 with 602 points - only 0.00% unknown
- deleting segment 8 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- mean border=73.5, 76 (76) missing vertices, mean dist 0.3 [0.5 (%32.4)->0.7 (%67.6))]
- %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.25 (0.07-->3.96) (max @ vno 85959 --> 84931)
- face area 0.28 +- 0.13 (0.00-->2.07)
- mean absolute distance = 0.30 +- 0.43
- 2549 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7122378.0, rms=13.46
- 001: dt: 0.5000, sse=6969587.0, rms=9.632 (0.000%)
- 002: dt: 0.5000, sse=7167657.0, rms=7.397 (0.000%)
- 003: dt: 0.5000, sse=7322853.5, rms=6.005 (0.000%)
- 004: dt: 0.5000, sse=7550652.5, rms=5.218 (0.000%)
- 005: dt: 0.5000, sse=7623704.5, rms=4.812 (0.000%)
- 006: dt: 0.5000, sse=7747985.0, rms=4.615 (0.000%)
- 007: dt: 0.5000, sse=7685367.0, rms=4.508 (0.000%)
- 008: dt: 0.5000, sse=7750102.0, rms=4.431 (0.000%)
- rms = 4.39, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=7652467.0, rms=4.392 (0.000%)
- 010: dt: 0.2500, sse=4784173.0, rms=2.985 (0.000%)
- 011: dt: 0.2500, sse=4326043.5, rms=2.510 (0.000%)
- 012: dt: 0.2500, sse=4078144.0, rms=2.400 (0.000%)
- 013: dt: 0.2500, sse=3992447.0, rms=2.310 (0.000%)
- rms = 2.27, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=3905625.2, rms=2.272 (0.000%)
- 015: dt: 0.1250, sse=3668625.2, rms=1.994 (0.000%)
- rms = 1.96, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=3627702.2, rms=1.956 (0.000%)
- positioning took 2.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 117 points - only 6.84% unknown
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 442 points - only 0.00% unknown
- deleting segment 8 with 79 points - only 0.00% unknown
- deleting segment 10 with 13 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- deleting segment 12 with 7 points - only 0.00% unknown
- mean border=78.3, 57 (28) missing vertices, mean dist -0.2 [0.3 (%80.2)->0.2 (%19.8))]
- %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.24 (0.05-->4.06) (max @ vno 85959 --> 84931)
- face area 0.35 +- 0.16 (0.00-->2.74)
- mean absolute distance = 0.20 +- 0.29
- 3006 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4675329.5, rms=6.32
- 017: dt: 0.5000, sse=4785857.0, rms=4.245 (0.000%)
- rms = 4.52, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4328110.5, rms=3.079 (0.000%)
- 019: dt: 0.2500, sse=4142340.2, rms=2.387 (0.000%)
- 020: dt: 0.2500, sse=4079477.2, rms=1.917 (0.000%)
- 021: dt: 0.2500, sse=4052949.8, rms=1.827 (0.000%)
- 022: dt: 0.2500, sse=3995944.5, rms=1.721 (0.000%)
- rms = 1.74, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.1250, sse=3944763.8, rms=1.639 (0.000%)
- 024: dt: 0.1250, sse=3872159.5, rms=1.526 (0.000%)
- rms = 1.52, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=3836854.0, rms=1.520 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 96 points - only 3.12% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 9 points - only 0.00% unknown
- deleting segment 4 with 459 points - only 0.00% unknown
- deleting segment 5 with 79 points - only 0.00% unknown
- deleting segment 7 with 13 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 7 points - only 0.00% unknown
- mean border=81.3, 52 (22) missing vertices, mean dist -0.1 [0.2 (%75.6)->0.2 (%24.4))]
- %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.24 (0.11-->4.10) (max @ vno 85959 --> 84931)
- face area 0.34 +- 0.15 (0.00-->2.91)
- mean absolute distance = 0.16 +- 0.23
- 3184 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4141655.2, rms=3.90
- rms = 4.10, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=3977442.5, rms=2.691 (0.000%)
- 027: dt: 0.2500, sse=3923864.0, rms=1.733 (0.000%)
- 028: dt: 0.2500, sse=3946174.0, rms=1.558 (0.000%)
- 029: dt: 0.2500, sse=3984213.8, rms=1.483 (0.000%)
- rms = 1.53, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=3940021.2, rms=1.418 (0.000%)
- 031: dt: 0.1250, sse=3874712.2, rms=1.343 (0.000%)
- rms = 1.34, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3874712.2, rms=1.343 (0.001%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 93 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 10 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- deleting segment 4 with 569 points - only 0.00% unknown
- deleting segment 5 with 13 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 8 points - only 0.00% unknown
- mean border=82.2, 57 (22) missing vertices, mean dist -0.0 [0.2 (%57.6)->0.2 (%42.4))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3897609.2, rms=1.72
- rms = 2.61, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=3959297.5, rms=1.154 (0.000%)
- 034: dt: 0.2500, sse=4099132.5, rms=1.003 (0.000%)
- rms = 1.01, time step reduction 2 of 3 to 0.125...
- rms = 0.99, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4099117.8, rms=0.993 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=49.7, 73 (73) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.3 (%100.0))]
- %17 local maxima, %53 large gradients and %26 min vals, 2014 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 1.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=29164570.0, rms=32.04
- 001: dt: 0.5000, sse=20762638.0, rms=26.471 (0.000%)
- 002: dt: 0.5000, sse=14961932.0, rms=21.843 (0.000%)
- 003: dt: 0.5000, sse=11112918.0, rms=18.077 (0.000%)
- 004: dt: 0.5000, sse=8727785.0, rms=15.075 (0.000%)
- 005: dt: 0.5000, sse=7370892.0, rms=12.763 (0.000%)
- 006: dt: 0.5000, sse=6597401.0, rms=11.017 (0.000%)
- 007: dt: 0.5000, sse=6173647.5, rms=9.571 (0.000%)
- 008: dt: 0.5000, sse=5945840.5, rms=8.309 (0.000%)
- 009: dt: 0.5000, sse=5854344.5, rms=7.197 (0.000%)
- 010: dt: 0.5000, sse=5870897.0, rms=6.260 (0.000%)
- 011: dt: 0.5000, sse=5988797.5, rms=5.498 (0.000%)
- 012: dt: 0.5000, sse=6106282.0, rms=4.923 (0.000%)
- 013: dt: 0.5000, sse=6300496.5, rms=4.538 (0.000%)
- 014: dt: 0.5000, sse=6406478.0, rms=4.294 (0.000%)
- 015: dt: 0.5000, sse=6513836.0, rms=4.120 (0.000%)
- 016: dt: 0.5000, sse=6540898.0, rms=4.013 (0.000%)
- 017: dt: 0.5000, sse=6618459.0, rms=3.932 (0.000%)
- rms = 3.90, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=6630461.5, rms=3.898 (0.000%)
- 019: dt: 0.2500, sse=4701764.5, rms=3.211 (0.000%)
- 020: dt: 0.2500, sse=4546906.5, rms=3.022 (0.000%)
- rms = 3.00, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4424072.0, rms=3.004 (0.000%)
- 022: dt: 0.1250, sse=4236301.5, rms=2.887 (0.000%)
- rms = 2.87, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4208064.0, rms=2.872 (0.000%)
- positioning took 2.8 minutes
- mean border=47.2, 963 (19) missing vertices, mean dist 0.2 [0.2 (%46.7)->0.6 (%53.3))]
- %33 local maxima, %41 large gradients and %21 min vals, 644 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4880360.5, rms=5.08
- 024: dt: 0.5000, sse=5088540.0, rms=4.148 (0.000%)
- 025: dt: 0.5000, sse=6467939.0, rms=4.028 (0.000%)
- rms = 4.02, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.5000, sse=6347704.5, rms=4.021 (0.000%)
- 027: dt: 0.2500, sse=5116655.0, rms=3.145 (0.000%)
- 028: dt: 0.2500, sse=5024321.0, rms=2.889 (0.000%)
- rms = 2.88, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.2500, sse=4912121.0, rms=2.883 (0.000%)
- 030: dt: 0.1250, sse=4724134.5, rms=2.713 (0.000%)
- rms = 2.69, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4710260.5, rms=2.691 (0.000%)
- positioning took 1.0 minutes
- mean border=45.0, 1140 (11) missing vertices, mean dist 0.1 [0.2 (%37.6)->0.4 (%62.4))]
- %52 local maxima, %22 large gradients and %21 min vals, 749 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4970060.5, rms=4.04
- 032: dt: 0.5000, sse=5146955.5, rms=3.864 (0.000%)
- rms = 3.97, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4821637.5, rms=3.143 (0.000%)
- 034: dt: 0.2500, sse=5015037.0, rms=2.855 (0.000%)
- rms = 2.82, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=4949331.5, rms=2.815 (0.000%)
- 036: dt: 0.1250, sse=4797166.0, rms=2.653 (0.000%)
- rms = 2.63, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=4798626.0, rms=2.632 (0.000%)
- positioning took 0.8 minutes
- mean border=43.9, 2366 (8) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.3 (%54.9))]
- %56 local maxima, %18 large gradients and %20 min vals, 563 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=4847700.0, rms=3.00
- rms = 3.57, time step reduction 1 of 3 to 0.250...
- 038: dt: 0.2500, sse=4723224.5, rms=2.750 (0.000%)
- 039: dt: 0.2500, sse=4867486.5, rms=2.658 (0.000%)
- rms = 2.63, time step reduction 2 of 3 to 0.125...
- 040: dt: 0.2500, sse=4947709.0, rms=2.633 (0.000%)
- 041: dt: 0.1250, sse=4861307.0, rms=2.519 (0.000%)
- rms = 2.50, time step reduction 3 of 3 to 0.062...
- 042: dt: 0.1250, sse=4874083.5, rms=2.496 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.area.pial
- vertex spacing 1.01 +- 0.42 (0.05-->7.30) (max @ vno 96822 --> 97898)
- face area 0.40 +- 0.30 (0.00-->5.17)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 135159 vertices processed
- 25000 of 135159 vertices processed
- 50000 of 135159 vertices processed
- 75000 of 135159 vertices processed
- 100000 of 135159 vertices processed
- 125000 of 135159 vertices processed
- 0 of 135159 vertices processed
- 25000 of 135159 vertices processed
- 50000 of 135159 vertices processed
- 75000 of 135159 vertices processed
- 100000 of 135159 vertices processed
- 125000 of 135159 vertices processed
- thickness calculation complete, 276:566 truncations.
- 30679 vertices at 0 distance
- 93349 vertices at 1 distance
- 85827 vertices at 2 distance
- 34579 vertices at 3 distance
- 9987 vertices at 4 distance
- 2713 vertices at 5 distance
- 761 vertices at 6 distance
- 255 vertices at 7 distance
- 103 vertices at 8 distance
- 49 vertices at 9 distance
- 51 vertices at 10 distance
- 41 vertices at 11 distance
- 28 vertices at 12 distance
- 17 vertices at 13 distance
- 14 vertices at 14 distance
- 11 vertices at 15 distance
- 11 vertices at 16 distance
- 5 vertices at 17 distance
- 7 vertices at 18 distance
- 4 vertices at 19 distance
- 7 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.thickness
- positioning took 13.6 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 19:11:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast lh Thu Aug 8 19:11:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- pctsurfcon --s sub004 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/pctsurfcon.log
- Thu Aug 8 19:11:39 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.1071/lh.wm.mgh --regheader sub004 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = lh
- ProjDist = -1
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- Done loading volume
- Computing registration from header.
- Using /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Done reading source surface
- Mapping Source Volume onto Source Subject Surface
- 1 -1 -1 -1
- using old
- Done mapping volume to surface
- Number of source voxels hit = 105076
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.1071/lh.wm.mgh
- Dim: 135159 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.1071/lh.gm.mgh --projfrac 0.3 --regheader sub004 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = lh
- ProjFrac = 0.3
- thickness = thickness
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- Done loading volume
- Computing registration from header.
- Using /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.thickness
- Done
- Mapping Source Volume onto Source Subject Surface
- 1 0.3 0.3 0.3
- using old
- Done mapping volume to surface
- Number of source voxels hit = 119956
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.1071/lh.gm.mgh
- Dim: 135159 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.1071/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.1071/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.w-g.pct.mgh
- ninputs = 2
- Checking inputs
- nframestot = 2
- Allocing output
- Done allocing
- Combining pairs
- nframes = 1
- Multiplying by 100.000000
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.w-g.pct.mgh --annot sub004 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/stats/lh.w-g.pct.stats --snr
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.w-g.pct.mgh --annot sub004 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 1000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.w-g.pct.mgh
- Vertex Area is 0.663051 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1873 1270.474
- 2 1002 caudalanteriorcingulate 1195 814.853
- 3 1003 caudalmiddlefrontal 3629 2498.512
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2317 1521.714
- 6 1006 entorhinal 944 635.092
- 7 1007 fusiform 4765 3211.987
- 8 1008 inferiorparietal 7354 4834.021
- 9 1009 inferiortemporal 5552 3670.319
- 10 1010 isthmuscingulate 1469 937.410
- 11 1011 lateraloccipital 8283 5314.176
- 12 1012 lateralorbitofrontal 3734 2451.514
- 13 1013 lingual 4691 3073.400
- 14 1014 medialorbitofrontal 2573 1702.272
- 15 1015 middletemporal 4979 3443.178
- 16 1016 parahippocampal 961 651.744
- 17 1017 paracentral 1859 1224.250
- 18 1018 parsopercularis 2500 1706.882
- 19 1019 parsorbitalis 1064 729.094
- 20 1020 parstriangularis 1638 1068.458
- 21 1021 pericalcarine 2087 1421.013
- 22 1022 postcentral 5894 3865.680
- 23 1023 posteriorcingulate 2014 1373.128
- 24 1024 precentral 6299 4124.202
- 25 1025 precuneus 5454 3619.139
- 26 1026 rostralanteriorcingulate 1293 860.160
- 27 1027 rostralmiddlefrontal 8240 5563.703
- 28 1028 superiorfrontal 10020 6801.779
- 29 1029 superiorparietal 7776 5048.333
- 30 1030 superiortemporal 5916 3914.814
- 31 1031 supramarginal 5501 3733.588
- 32 1032 frontalpole 325 214.163
- 33 1033 temporalpole 871 576.159
- 34 1034 transversetemporal 621 378.440
- 35 1035 insula 3319 2115.528
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 19:11:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub004 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Saving annotation colortable ../label/aparc.annot.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 1873 1270 3113 2.460 0.507 0.121 0.033 19 2.5 bankssts
- 1195 815 2469 2.511 0.794 0.162 0.056 26 2.9 caudalanteriorcingulate
- 3629 2499 7032 2.483 0.467 0.122 0.033 48 5.1 caudalmiddlefrontal
- 2317 1522 3117 1.871 0.427 0.172 0.078 45 6.3 cuneus
- 944 635 3187 3.749 0.573 0.143 0.067 16 2.9 entorhinal
- 4765 3212 9867 2.769 0.539 0.147 0.048 85 9.6 fusiform
- 7354 4834 13223 2.466 0.443 0.134 0.096 129 13.0 inferiorparietal
- 5552 3670 11056 2.666 0.646 0.138 0.053 91 11.0 inferiortemporal
- 1469 937 2706 2.461 0.838 0.156 0.061 28 3.5 isthmuscingulate
- 8283 5314 12632 2.146 0.478 0.155 1.364 623 19.1 lateraloccipital
- 3734 2452 7367 2.723 0.656 0.144 0.057 68 8.8 lateralorbitofrontal
- 4691 3073 7039 2.066 0.574 0.155 0.070 109 13.1 lingual
- 2573 1702 4338 2.204 0.731 0.156 0.081 79 7.1 medialorbitofrontal
- 4979 3443 12010 2.837 0.631 0.154 0.062 122 10.9 middletemporal
- 961 652 2469 3.224 0.717 0.148 0.083 135 3.9 parahippocampal
- 1859 1224 3327 2.514 0.492 0.125 0.036 19 2.8 paracentral
- 2500 1707 5066 2.535 0.431 0.122 0.036 36 3.6 parsopercularis
- 1064 729 2650 2.734 0.495 0.155 0.055 22 2.3 parsorbitalis
- 1638 1068 2952 2.496 0.529 0.127 0.044 21 2.8 parstriangularis
- 2087 1421 2338 1.823 0.491 0.125 0.042 19 3.7 pericalcarine
- 5894 3866 9545 2.162 0.549 0.123 0.036 69 8.6 postcentral
- 2014 1373 3556 2.338 0.733 0.144 0.047 37 4.2 posteriorcingulate
- 6299 4124 12397 2.674 0.536 0.116 0.034 64 8.4 precentral
- 5454 3619 9842 2.466 0.583 0.139 0.045 79 9.9 precuneus
- 1293 860 2669 2.574 0.729 0.156 0.067 27 3.1 rostralanteriorcingulate
- 8240 5564 15075 2.363 0.534 0.150 0.053 166 16.9 rostralmiddlefrontal
- 10020 6802 21554 2.769 0.568 0.130 0.037 118 15.8 superiorfrontal
- 7776 5048 12523 2.274 0.384 0.134 0.041 109 13.1 superiorparietal
- 5916 3915 12973 2.948 0.601 0.131 0.043 83 10.7 superiortemporal
- 5501 3734 10972 2.590 0.543 0.144 0.050 98 10.2 supramarginal
- 325 214 847 2.818 0.484 0.195 0.074 13 0.9 frontalpole
- 871 576 3018 3.661 0.594 0.140 0.054 12 1.9 temporalpole
- 621 378 1086 2.663 0.424 0.146 0.056 9 1.4 transversetemporal
- 3319 2116 6760 3.042 0.686 0.120 0.067 84 6.6 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 19:12:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub004 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs...
- reading color table from GCSA file....
- average std = 3.9 0.2 using min determinant for regularization = 0.000
- 0 singular and 1066 ill-conditioned covariance matrices regularized
- input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 19 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9211 changed, 135159 examined...
- 001: 2395 changed, 35366 examined...
- 002: 742 changed, 12331 examined...
- 003: 347 changed, 4188 examined...
- 004: 159 changed, 1915 examined...
- 005: 82 changed, 907 examined...
- 006: 48 changed, 479 examined...
- 007: 26 changed, 252 examined...
- 008: 16 changed, 140 examined...
- 009: 4 changed, 74 examined...
- 010: 1 changed, 22 examined...
- 011: 0 changed, 7 examined...
- 8 labels changed using aseg
- 000: 298 total segments, 216 labels (2854 vertices) changed
- 001: 100 total segments, 18 labels (137 vertices) changed
- 002: 83 total segments, 1 labels (2 vertices) changed
- 003: 82 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 137 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 907 vertices marked for relabeling...
- 907 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 11 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 19:13:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub004 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
- Saving annotation colortable ../label/aparc.annot.a2009s.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 1396 934 2636 2.401 0.612 0.154 0.050 27 2.9 G_and_S_frontomargin
- 1601 1086 3258 2.440 0.475 0.160 0.058 30 3.4 G_and_S_occipital_inf
- 1504 937 2868 2.478 0.566 0.131 0.039 19 2.5 G_and_S_paracentral
- 1267 837 2881 2.812 0.461 0.150 0.051 18 2.5 G_and_S_subcentral
- 638 453 1720 2.916 0.504 0.217 0.103 28 2.3 G_and_S_transv_frontopol
- 2198 1500 4104 2.439 0.647 0.141 0.054 34 4.9 G_and_S_cingul-Ant
- 1377 944 2886 2.739 0.569 0.139 0.047 21 2.4 G_and_S_cingul-Mid-Ant
- 1460 1005 2651 2.571 0.475 0.139 0.044 23 2.7 G_and_S_cingul-Mid-Post
- 667 437 1747 2.912 0.773 0.175 0.062 15 1.8 G_cingul-Post-dorsal
- 270 166 412 2.028 0.756 0.155 0.068 5 0.8 G_cingul-Post-ventral
- 2100 1361 2741 1.772 0.405 0.175 0.087 43 6.5 G_cuneus
- 1481 990 3522 2.742 0.529 0.138 0.047 28 2.8 G_front_inf-Opercular
- 359 232 968 3.003 0.408 0.164 0.067 7 1.1 G_front_inf-Orbital
- 917 598 2031 2.676 0.442 0.148 0.056 18 2.0 G_front_inf-Triangul
- 4733 3207 10682 2.588 0.481 0.159 0.054 112 10.6 G_front_middle
- 6669 4486 16521 2.948 0.530 0.143 0.044 98 12.6 G_front_sup
- 561 334 1288 3.099 0.752 0.148 0.170 48 1.8 G_Ins_lg_and_S_cent_ins
- 796 497 2291 3.452 0.543 0.133 0.060 14 1.8 G_insular_short
- 2663 1685 4876 2.363 0.458 0.154 0.058 57 6.3 G_occipital_middle
- 1807 1132 3051 2.284 0.447 0.167 0.070 40 4.9 G_occipital_sup
- 1623 1055 3797 2.837 0.481 0.160 0.057 45 3.9 G_oc-temp_lat-fusifor
- 3275 2082 5033 2.023 0.618 0.166 0.078 94 9.9 G_oc-temp_med-Lingual
- 1672 1132 5170 3.570 0.659 0.158 0.075 147 5.7 G_oc-temp_med-Parahip
- 2531 1646 6019 2.733 0.650 0.164 0.070 68 7.3 G_orbital
- 2340 1534 5411 2.688 0.461 0.153 0.224 73 5.9 G_pariet_inf-Angular
- 2896 1961 6683 2.737 0.542 0.164 0.064 73 6.5 G_pariet_inf-Supramar
- 2966 1919 5555 2.343 0.374 0.134 0.037 44 4.5 G_parietal_sup
- 2186 1415 4051 2.244 0.477 0.128 0.036 33 3.4 G_postcentral
- 2160 1416 5411 2.883 0.415 0.119 0.035 29 2.8 G_precentral
- 2796 1824 5989 2.535 0.556 0.152 0.051 52 6.0 G_precuneus
- 849 579 1874 2.384 0.577 0.218 0.122 56 3.7 G_rectus
- 364 225 575 2.588 0.771 0.147 0.100 8 1.0 G_subcallosal
- 503 307 1031 2.714 0.486 0.152 0.062 8 1.3 G_temp_sup-G_T_transv
- 2264 1475 6380 3.165 0.620 0.150 0.056 45 5.2 G_temp_sup-Lateral
- 526 359 1559 3.789 0.645 0.120 0.043 5 0.8 G_temp_sup-Plan_polar
- 1185 805 2246 2.457 0.454 0.113 0.026 10 1.3 G_temp_sup-Plan_tempo
- 2910 1928 7174 2.803 0.754 0.152 0.068 66 7.5 G_temporal_inf
- 2959 2040 8328 2.949 0.608 0.169 0.080 101 7.8 G_temporal_middle
- 405 259 759 2.700 0.514 0.119 0.039 4 0.7 Lat_Fis-ant-Horizont
- 352 248 634 2.413 0.347 0.107 0.023 3 0.3 Lat_Fis-ant-Vertical
- 1329 876 1937 2.697 0.473 0.138 0.053 20 2.8 Lat_Fis-post
- 2480 1529 3036 1.855 0.431 0.165 4.424 521 6.8 Pole_occipital
- 2001 1332 6174 3.304 0.633 0.145 0.063 36 5.4 Pole_temporal
- 2708 1853 3503 2.065 0.653 0.127 0.046 28 5.6 S_calcarine
- 2741 1839 3466 2.137 0.625 0.108 0.032 19 3.5 S_central
- 1123 773 1756 2.365 0.383 0.106 0.032 8 1.3 S_cingul-Marginalis
- 734 478 1222 3.037 0.420 0.116 0.039 5 1.1 S_circular_insula_ant
- 1415 951 2343 2.822 0.597 0.090 0.020 6 1.3 S_circular_insula_inf
- 1742 1161 2572 2.524 0.427 0.108 0.026 10 2.0 S_circular_insula_sup
- 1386 942 2222 2.610 0.417 0.101 0.021 8 1.3 S_collat_transv_ant
- 499 331 699 2.472 0.448 0.160 0.059 7 1.1 S_collat_transv_post
- 2074 1431 2869 2.152 0.411 0.109 0.025 15 2.1 S_front_inf
- 1541 1041 2177 2.112 0.477 0.126 0.052 23 2.4 S_front_middle
- 2566 1814 4342 2.385 0.431 0.106 0.024 20 2.7 S_front_sup
- 59 41 79 1.961 0.224 0.140 0.030 0 0.1 S_interm_prim-Jensen
- 2718 1800 3701 2.275 0.317 0.121 0.035 25 3.8 S_intrapariet_and_P_trans
- 1341 892 1690 2.078 0.367 0.134 0.038 14 2.0 S_oc_middle_and_Lunatus
- 1413 917 1945 2.134 0.421 0.135 0.041 18 2.1 S_oc_sup_and_transversal
- 953 660 1285 2.357 0.410 0.143 0.040 10 1.5 S_occipital_ant
- 850 590 1209 2.362 0.343 0.132 0.037 9 1.2 S_oc-temp_lat
- 1717 1211 2875 2.536 0.537 0.131 0.038 19 2.6 S_oc-temp_med_and_Lingual
- 501 334 706 2.176 0.383 0.119 0.035 5 0.8 S_orbital_lateral
- 853 548 1235 2.420 0.973 0.104 0.044 15 1.4 S_orbital_med-olfact
- 1380 930 2359 2.528 0.587 0.133 0.046 17 2.5 S_orbital-H_Shaped
- 1827 1228 2672 2.404 0.613 0.134 0.040 22 2.9 S_parieto_occipital
- 1432 910 1393 1.776 0.662 0.140 0.045 26 2.2 S_pericallosal
- 3000 2000 4109 2.174 0.409 0.112 0.028 24 3.5 S_postcentral
- 1493 995 2349 2.436 0.396 0.106 0.027 11 1.6 S_precentral-inf-part
- 1082 729 1339 2.116 0.292 0.087 0.015 4 0.8 S_precentral-sup-part
- 663 432 931 1.914 0.659 0.144 0.066 13 1.6 S_suborbital
- 1084 708 1453 2.208 0.469 0.125 0.040 11 1.6 S_subparietal
- 1979 1301 2706 2.481 0.505 0.134 0.039 22 3.2 S_temporal_inf
- 6800 4558 11107 2.514 0.497 0.120 0.034 68 9.3 S_temporal_sup
- 300 203 499 2.864 0.358 0.157 0.038 4 0.5 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 19:13:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub004 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/5.3.0/average/lh.DKTatlas40.gcs...
- reading color table from GCSA file....
- average std = 0.9 using min determinant for regularization = 0.007
- 0 singular and 293 ill-conditioned covariance matrices regularized
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 909 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3008 changed, 135159 examined...
- 001: 715 changed, 12549 examined...
- 002: 166 changed, 3892 examined...
- 003: 54 changed, 932 examined...
- 004: 22 changed, 336 examined...
- 005: 6 changed, 124 examined...
- 006: 4 changed, 40 examined...
- 007: 0 changed, 18 examined...
- 105 labels changed using aseg
- 000: 65 total segments, 32 labels (224 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 35 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 578 vertices marked for relabeling...
- 578 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 2 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 19:14:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub004 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
- Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 1725 1161 3276 2.555 0.691 0.143 0.047 28 3.4 caudalanteriorcingulate
- 3743 2570 7251 2.482 0.467 0.123 0.034 51 5.3 caudalmiddlefrontal
- 3110 2031 4388 1.961 0.447 0.166 0.073 60 8.2 cuneus
- 944 635 3182 3.757 0.577 0.147 0.060 14 2.3 entorhinal
- 4241 2875 8669 2.746 0.520 0.147 0.047 77 8.3 fusiform
- 6867 4507 12347 2.473 0.439 0.132 0.098 117 11.7 inferiorparietal
- 5674 3763 11557 2.676 0.653 0.136 0.053 91 11.3 inferiortemporal
- 1495 950 2801 2.499 0.843 0.158 0.062 30 3.7 isthmuscingulate
- 8695 5566 13219 2.133 0.480 0.155 1.301 630 19.7 lateraloccipital
- 4058 2663 8305 2.719 0.686 0.146 0.061 87 10.0 lateralorbitofrontal
- 4713 3093 7069 2.063 0.577 0.155 0.070 110 13.1 lingual
- 2193 1436 3813 2.173 0.691 0.167 0.091 77 6.9 medialorbitofrontal
- 6688 4591 14762 2.745 0.621 0.149 0.057 143 13.5 middletemporal
- 947 640 2407 3.217 0.717 0.150 0.085 135 4.0 parahippocampal
- 2148 1417 3974 2.572 0.505 0.124 0.034 21 3.1 paracentral
- 2210 1501 4470 2.556 0.415 0.123 0.037 33 3.3 parsopercularis
- 1232 821 2889 2.864 0.491 0.141 0.051 20 2.7 parsorbitalis
- 2174 1460 3784 2.389 0.493 0.127 0.040 28 3.5 parstriangularis
- 2047 1399 2300 1.829 0.492 0.126 0.042 19 3.6 pericalcarine
- 6572 4322 10563 2.178 0.536 0.122 0.035 75 9.4 postcentral
- 2226 1512 3813 2.342 0.710 0.144 0.047 39 4.5 posteriorcingulate
- 6207 4058 12219 2.692 0.531 0.116 0.034 61 8.4 precentral
- 5346 3540 9700 2.460 0.581 0.139 0.044 78 9.7 precuneus
- 1621 1086 3145 2.510 0.754 0.154 0.063 32 3.6 rostralanteriorcingulate
- 5726 3838 10311 2.323 0.536 0.147 0.052 111 11.4 rostralmiddlefrontal
- 11292 7695 24345 2.716 0.583 0.137 0.042 164 19.5 superiorfrontal
- 6006 3898 9706 2.303 0.360 0.133 0.040 81 9.7 superiorparietal
- 8270 5483 18699 2.965 0.660 0.135 0.049 126 17.0 superiortemporal
- 5391 3655 10698 2.585 0.554 0.144 0.051 97 10.1 supramarginal
- 602 366 1053 2.649 0.414 0.145 0.057 9 1.4 transversetemporal
- 2847 1835 6060 3.091 0.624 0.111 0.056 63 4.2 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 19:15:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 2 found - 2 modified | TOTAL: 2
- pass 2 (xy+): 0 found - 2 modified | TOTAL: 2
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 2
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (yz-): 3 found - 3 modified | TOTAL: 5
- pass 2 (yz-): 0 found - 3 modified | TOTAL: 5
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 7
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 7
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 7
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 2 found - 2 modified | TOTAL: 2
- pass 2 (--): 0 found - 2 modified | TOTAL: 2
- pass 1 (-+): 1 found - 1 modified | TOTAL: 3
- pass 2 (-+): 0 found - 1 modified | TOTAL: 3
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 10 (out of 257144: 0.003889)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 40: 8 vertices, 11 faces
- slice 50: 2546 vertices, 2690 faces
- slice 60: 8110 vertices, 8329 faces
- slice 70: 15473 vertices, 15799 faces
- slice 80: 25287 vertices, 25634 faces
- slice 90: 36088 vertices, 36467 faces
- slice 100: 47369 vertices, 47726 faces
- slice 110: 59335 vertices, 59712 faces
- slice 120: 70482 vertices, 70874 faces
- slice 130: 82279 vertices, 82710 faces
- slice 140: 93386 vertices, 93796 faces
- slice 150: 103523 vertices, 103869 faces
- slice 160: 111759 vertices, 112041 faces
- slice 170: 119241 vertices, 119525 faces
- slice 180: 125950 vertices, 126205 faces
- slice 190: 131786 vertices, 132007 faces
- slice 200: 136082 vertices, 136207 faces
- slice 210: 136584 vertices, 136616 faces
- slice 220: 136584 vertices, 136616 faces
- slice 230: 136584 vertices, 136616 faces
- slice 240: 136584 vertices, 136616 faces
- slice 250: 136584 vertices, 136616 faces
- using the conformed surface RAS to save vertex points...
- writing ../surf/rh.orig.nofix
- using vox2ras matrix:
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- rm -f ../mri/filled-pretess127.mgz
- mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix
- counting number of connected components...
- 136584 voxel in cpt #1: X=-32 [v=136584,e=409848,f=273232] located at (29.086987, -9.569188, 36.788971)
- For the whole surface: X=-32 [v=136584,e=409848,f=273232]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 19:15:12 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 rh Thu Aug 8 19:15:16 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- avg radius = 46.1 mm, total surface area = 71737 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.101 (target=0.015)
step 005: RMS=0.074 (target=0.015)
step 010: RMS=0.054 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.036 (target=0.015)
step 030: RMS=0.032 (target=0.015)
step 035: RMS=0.030 (target=0.015)
step 040: RMS=0.027 (target=0.015)
step 045: RMS=0.026 (target=0.015)
step 050: RMS=0.025 (target=0.015)
step 055: RMS=0.025 (target=0.015)
step 060: RMS=0.025 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 19:15:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.99 +- 0.57 (0.00-->7.66) (max @ vno 55410 --> 56658)
- face area 0.02 +- 0.03 (-0.28-->0.76)
- scaling brain by 0.307...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=177.088, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.827, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.266, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.527, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.687, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.793, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.869, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.928, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.979, avgs=0
- 045/300: dt: 0.9000, rms radial error=170.028, avgs=0
- 050/300: dt: 0.9000, rms radial error=169.078, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.130, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.186, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.245, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.310, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.378, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.452, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.531, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.614, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.703, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.797, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.896, avgs=0
- 110/300: dt: 0.9000, rms radial error=158.000, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.110, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.218, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.343, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.455, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.599, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.735, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.875, avgs=0
- 150/300: dt: 0.9000, rms radial error=151.018, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.167, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.319, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.475, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.636, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.805, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.974, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.148, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.329, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.513, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.706, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.901, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.101, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.304, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.512, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.724, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.942, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.163, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.391, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.622, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.856, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.094, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.339, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.586, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.839, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.094, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.354, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.619, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.887, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.159, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.436, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 16058.43
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
- epoch 2 (K=40.0), pass 1, starting sse = 2706.63
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
- epoch 3 (K=160.0), pass 1, starting sse = 280.11
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.05/10 = 0.00466
- epoch 4 (K=640.0), pass 1, starting sse = 18.10
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/13 = 0.00618
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.08 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 19:20:28 CEST 2013
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub004 rh
- reading spherical homeomorphism from 'qsphere.nofix'
- using genetic algorithm with optimized parameters
- setting seed for random number genererator to 1234
- *************************************************************
- Topology Correction Parameters
- retessellation mode: genetic search
- number of patches/generation : 10
- number of generations : 10
- surface mri loglikelihood coefficient : 1.0
- volume mri loglikelihood coefficient : 10.0
- normal dot loglikelihood coefficient : 1.0
- quadratic curvature loglikelihood coefficient : 1.0
- volume resolution : 2
- eliminate vertices during search : 1
- initial patch selection : 1
- select all defect vertices : 0
- ordering dependant retessellation: 0
- use precomputed edge table : 0
- smooth retessellated patch : 2
- match retessellated patch : 1
- verbose mode : 0
- *************************************************************
- INFO: assuming .mgz format
- $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- before topology correction, eno=-32 (nv=136584, nf=273232, ne=409848, g=17)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 10 iterations
- marking ambiguous vertices...
- 3545 ambiguous faces found in tessellation
- segmenting defects...
- 19 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 19 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7000 (-4.8500)
- -vertex loglikelihood: -6.6091 (-3.3045)
- -normal dot loglikelihood: -3.6258 (-3.6258)
- -quad curv loglikelihood: -6.5200 (-3.2600)
- Total Loglikelihood : -26.4549
- CORRECTING DEFECT 0 (vertices=28, convex hull=26)
- After retessellation of defect 0, euler #=-16 (134480,402738,268242) : difference with theory (-16) = 0
- CORRECTING DEFECT 1 (vertices=38, convex hull=61)
- After retessellation of defect 1, euler #=-15 (134500,402820,268305) : difference with theory (-15) = 0
- CORRECTING DEFECT 2 (vertices=30, convex hull=62)
- After retessellation of defect 2, euler #=-14 (134509,402871,268348) : difference with theory (-14) = 0
- CORRECTING DEFECT 3 (vertices=714, convex hull=340)
- After retessellation of defect 3, euler #=-13 (134653,403495,268829) : difference with theory (-13) = 0
- CORRECTING DEFECT 4 (vertices=14, convex hull=20)
- Warning - incorrect dp selected!!!!(-77.540500 >= -77.540502 )
- After retessellation of defect 4, euler #=-12 (134655,403506,268839) : difference with theory (-12) = 0
- CORRECTING DEFECT 5 (vertices=49, convex hull=39)
- After retessellation of defect 5, euler #=-11 (134662,403540,268867) : difference with theory (-11) = 0
- CORRECTING DEFECT 6 (vertices=267, convex hull=148)
- After retessellation of defect 6, euler #=-10 (134682,403657,268965) : difference with theory (-10) = 0
- CORRECTING DEFECT 7 (vertices=86, convex hull=30)
- After retessellation of defect 7, euler #=-9 (134689,403684,268986) : difference with theory (-9) = 0
- CORRECTING DEFECT 8 (vertices=38, convex hull=73)
- After retessellation of defect 8, euler #=-8 (134699,403742,269035) : difference with theory (-8) = 0
- CORRECTING DEFECT 9 (vertices=443, convex hull=335)
- After retessellation of defect 9, euler #=-7 (134783,404153,269363) : difference with theory (-7) = 0
- CORRECTING DEFECT 10 (vertices=25, convex hull=43)
- After retessellation of defect 10, euler #=-6 (134793,404197,269398) : difference with theory (-6) = 0
- CORRECTING DEFECT 11 (vertices=127, convex hull=91)
- After retessellation of defect 11, euler #=-5 (134805,404275,269465) : difference with theory (-5) = 0
- CORRECTING DEFECT 12 (vertices=75, convex hull=83)
- After retessellation of defect 12, euler #=-4 (134830,404388,269554) : difference with theory (-4) = 0
- CORRECTING DEFECT 13 (vertices=18, convex hull=42)
- After retessellation of defect 13, euler #=-3 (134843,404441,269595) : difference with theory (-3) = 0
- CORRECTING DEFECT 14 (vertices=55, convex hull=44)
- After retessellation of defect 14, euler #=-2 (134865,404524,269657) : difference with theory (-2) = 0
- CORRECTING DEFECT 15 (vertices=27, convex hull=48)
- After retessellation of defect 15, euler #=-1 (134875,404570,269694) : difference with theory (-1) = 0
- CORRECTING DEFECT 16 (vertices=20, convex hull=21)
- After retessellation of defect 16, euler #=0 (134878,404585,269707) : difference with theory (0) = 0
- CORRECTING DEFECT 17 (vertices=14, convex hull=22)
- After retessellation of defect 17, euler #=1 (134880,404598,269719) : difference with theory (1) = 0
- CORRECTING DEFECT 18 (vertices=36, convex hull=81)
- After retessellation of defect 18, euler #=2 (134900,404694,269796) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.23 (0.10-->12.19) (max @ vno 56116 --> 57289)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.23 (0.10-->12.19) (max @ vno 56116 --> 57289)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 96 mutations (35.3%), 176 crossovers (64.7%), 295 vertices were eliminated
- building final representation...
- 1684 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=134900, nf=269796, ne=404694, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 18.4 minutes
- 0 defective edges
- removing intersecting faces
- 000: 297 intersecting
- 001: 11 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 134900 - 404694 + 269796 = 2 --> 0 holes
- F =2V-4: 269796 = 269800-4 (0)
- 2E=3F: 809388 = 809388 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 82 intersecting
- 001: 2 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 19:39:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub004 rh
- only generating white matter surface
- not using aparc to prevent surfaces crossing the midline
- INFO: assuming MGZ format for volumes.
- using brain.finalsurfs as T1 volume...
- $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- 16676 bright wm thresholded.
- 447 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.orig...
- computing class statistics...
- border white: 249466 voxels (1.49%)
- border gray 280050 voxels (1.67%)
- WM (92.0): 93.5 +- 9.9 [70.0 --> 110.0]
- GM (76.0) : 73.7 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 45.7 (was 70)
- setting MAX_BORDER_WHITE to 114.9 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 32.5 (was 40)
- setting MAX_GRAY to 95.1 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 19.2 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.02-->5.91) (max @ vno 57288 --> 57289)
- face area 0.28 +- 0.12 (0.00-->5.12)
- mean absolute distance = 0.63 +- 0.72
- 3896 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 93.1, mean outside = 68.7
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=73.5, 23 (23) missing vertices, mean dist 0.3 [0.4 (%33.2)->0.7 (%66.8))]
- %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.06-->7.18) (max @ vno 57289 --> 57288)
- face area 0.28 +- 0.13 (0.00-->4.70)
- mean absolute distance = 0.28 +- 0.44
- 2547 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7040229.0, rms=13.32
- 001: dt: 0.5000, sse=6971563.0, rms=9.527 (0.000%)
- 002: dt: 0.5000, sse=7325030.5, rms=7.370 (0.000%)
- 003: dt: 0.5000, sse=7417160.0, rms=6.010 (0.000%)
- 004: dt: 0.5000, sse=7768296.5, rms=5.243 (0.000%)
- 005: dt: 0.5000, sse=7789822.0, rms=4.835 (0.000%)
- 006: dt: 0.5000, sse=7983950.0, rms=4.631 (0.000%)
- 007: dt: 0.5000, sse=7887380.5, rms=4.523 (0.000%)
- 008: dt: 0.5000, sse=7982241.5, rms=4.455 (0.000%)
- rms = 4.42, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=7851135.5, rms=4.419 (0.000%)
- 010: dt: 0.2500, sse=4984594.5, rms=2.987 (0.000%)
- 011: dt: 0.2500, sse=4461930.5, rms=2.495 (0.000%)
- 012: dt: 0.2500, sse=4188860.2, rms=2.370 (0.000%)
- 013: dt: 0.2500, sse=4096027.2, rms=2.271 (0.000%)
- rms = 2.23, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4012923.2, rms=2.232 (0.000%)
- 015: dt: 0.1250, sse=3785699.5, rms=1.980 (0.000%)
- rms = 1.95, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=3738518.8, rms=1.948 (0.000%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- mean border=77.8, 52 (4) missing vertices, mean dist -0.2 [0.3 (%78.3)->0.2 (%21.7))]
- %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.12-->7.55) (max @ vno 57289 --> 57288)
- face area 0.35 +- 0.16 (0.00-->6.60)
- mean absolute distance = 0.20 +- 0.29
- 3171 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4629504.5, rms=5.80
- 017: dt: 0.5000, sse=4905366.0, rms=3.998 (0.000%)
- rms = 4.49, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4417587.0, rms=2.826 (0.000%)
- 019: dt: 0.2500, sse=4234190.0, rms=2.291 (0.000%)
- 020: dt: 0.2500, sse=4180524.8, rms=1.921 (0.000%)
- rms = 1.88, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4156580.5, rms=1.881 (0.000%)
- 022: dt: 0.1250, sse=4016568.8, rms=1.655 (0.000%)
- rms = 1.62, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=3972529.2, rms=1.616 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=80.5, 30 (2) missing vertices, mean dist -0.1 [0.2 (%72.4)->0.2 (%27.6))]
- %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.08-->7.55) (max @ vno 57289 --> 57288)
- face area 0.34 +- 0.16 (0.00-->7.01)
- mean absolute distance = 0.17 +- 0.24
- 3593 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4238288.0, rms=3.71
- rms = 3.96, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=4104078.5, rms=2.589 (0.000%)
- 025: dt: 0.2500, sse=4077315.0, rms=1.742 (0.000%)
- 026: dt: 0.2500, sse=4105015.0, rms=1.607 (0.000%)
- 027: dt: 0.2500, sse=4122170.5, rms=1.543 (0.000%)
- rms = 1.58, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.1250, sse=4078453.5, rms=1.485 (0.000%)
- 029: dt: 0.1250, sse=4013955.5, rms=1.415 (0.000%)
- rms = 1.42, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=4013955.5, rms=1.415 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=81.4, 34 (2) missing vertices, mean dist -0.0 [0.2 (%57.2)->0.2 (%42.8))]
- %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4039668.2, rms=1.81
- rms = 2.63, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=4116279.5, rms=1.239 (0.000%)
- 032: dt: 0.2500, sse=4276780.0, rms=1.054 (0.000%)
- rms = 1.06, time step reduction 2 of 3 to 0.125...
- rms = 1.05, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=4276212.5, rms=1.045 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 17 non-cortical segments detected
- only using segment with 1628 vertices
- erasing segment 0 (vno[0] = 49125)
- erasing segment 2 (vno[0] = 76967)
- erasing segment 3 (vno[0] = 79334)
- erasing segment 4 (vno[0] = 80465)
- erasing segment 5 (vno[0] = 92259)
- erasing segment 6 (vno[0] = 93512)
- erasing segment 7 (vno[0] = 95268)
- erasing segment 8 (vno[0] = 96162)
- erasing segment 9 (vno[0] = 96270)
- erasing segment 10 (vno[0] = 98448)
- erasing segment 11 (vno[0] = 100268)
- erasing segment 12 (vno[0] = 102179)
- erasing segment 13 (vno[0] = 104871)
- erasing segment 14 (vno[0] = 104924)
- erasing segment 15 (vno[0] = 105730)
- erasing segment 16 (vno[0] = 106500)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.area
- vertex spacing 0.89 +- 0.25 (0.08-->7.55) (max @ vno 57289 --> 57288)
- face area 0.33 +- 0.16 (0.00-->6.96)
- refinement took 6.6 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 19:45:35 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 19:45:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 46.5 mm, total surface area = 82318 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.116 (target=0.015)
step 005: RMS=0.081 (target=0.015)
step 010: RMS=0.058 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.033 (target=0.015)
step 030: RMS=0.029 (target=0.015)
step 035: RMS=0.024 (target=0.015)
step 040: RMS=0.021 (target=0.015)
step 045: RMS=0.019 (target=0.015)
step 050: RMS=0.018 (target=0.015)
step 055: RMS=0.017 (target=0.015)
step 060: RMS=0.016 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 157 vertices thresholded to be in k1 ~ [-0.18 0.85], k2 ~ [-0.14 0.08]
- total integrated curvature = 0.600*4pi (7.539) --> 0 handles
- ICI = 1.5, FI = 8.1, variation=142.348
- 121 vertices thresholded to be in [-0.05 0.01]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 104 vertices thresholded to be in [-0.12 0.21]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.021
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 19:48:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub004 rh curv sulc
- Toggling save flag on curvature files [ ok ]
- Outputting results using filestem [ ../stats/rh.curv.stats ]
- Toggling save flag on curvature files [ ok ]
- Setting surface [ sub004/rh.smoothwm ]
- Reading surface... [ ok ]
- Setting texture [ curv ]
- Reading texture... [ ok ]
- Setting texture [ sulc ]
- Reading texture...Gb_filter = 0
- [ ok ]
- Calculating Discrete Principal Curvatures...
- Determining geometric order for vertex faces... [####################] [ ok ]
- Determining KH curvatures... [####################] [ ok ]
- Determining k1k2 curvatures... [####################] [ ok ]
- deltaViolations [ 221 ]
- Gb_filter = 0
- WARN: S lookup min: -0.202156
- WARN: S explicit min: 0.000000 vertex = 264
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 19:48:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- scaling brain by 0.285...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.95
- pass 1: epoch 2 of 3 starting distance error %20.92
- unfolding complete - removing small folds...
- starting distance error %20.84
- removing remaining folds...
- final distance error %20.85
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.02 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 20:49:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_register -curv ../surf/rh.sphere /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg
- using smoothwm curvature for final alignment
- $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading surface from ../surf/rh.sphere...
- reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
- MRISregister() -------
- max_passes = 4
- min_degrees = 0.500000
- max_degrees = 64.000000
- nangles = 8
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height -1.000000
- momentum 0.950000
- nbhd_size -10
- max_nbrs 10
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 16 (10)
- use curv 16
- no sulc 0
- no rigid align 0
- mris->nsize 1
- mris->hemisphere 1
- randomSeed 0
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
- using quadratic fit line minimization
- --------------------
- 1 Reading rh.sulc
- curvature mean = -0.000, std = 0.595
- curvature mean = 0.027, std = 0.936
- curvature mean = 0.021, std = 0.859
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 379399.3, tmin=1.0809
- d=32.00 min @ (-8.00, -8.00, 8.00) sse = 314962.3, tmin=2.1608
- d=8.00 min @ (2.00, 2.00, -2.00) sse = 308356.1, tmin=4.3497
- d=2.00 min @ (-0.50, -0.50, 0.00) sse = 308035.9, tmin=6.5492
- d=1.00 min @ (0.25, 0.00, -0.25) sse = 307985.7, tmin=7.6687
- d=0.50 min @ (0.00, 0.00, 0.12) sse = 307970.8, tmin=8.8422
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 8.84 min
- curvature mean = 0.000, std = 0.951
- curvature mean = 0.011, std = 0.941
- curvature mean = -0.007, std = 0.955
- curvature mean = 0.005, std = 0.973
- curvature mean = -0.007, std = 0.956
- curvature mean = 0.002, std = 0.988
- 2 Reading smoothwm
- curvature mean = -0.023, std = 0.305
- curvature mean = 0.005, std = 0.070
- curvature mean = 0.062, std = 0.334
- curvature mean = 0.005, std = 0.084
- curvature mean = 0.025, std = 0.515
- curvature mean = 0.005, std = 0.090
- curvature mean = 0.015, std = 0.647
- curvature mean = 0.006, std = 0.092
- curvature mean = 0.004, std = 0.756
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 21:19:03 CEST 2013
- mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- reading surface from ../surf/rh.white...
- writing curvature file ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Thu Aug 8 21:19:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/rh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/rh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc rh Thu Aug 8 21:19:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub004 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
- reading color table from GCSA file....
- average std = 0.7 using min determinant for regularization = 0.006
- 0 singular and 311 ill-conditioned covariance matrices regularized
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 1048 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2989 changed, 134900 examined...
- 001: 670 changed, 12574 examined...
- 002: 159 changed, 3796 examined...
- 003: 59 changed, 976 examined...
- 004: 31 changed, 378 examined...
- 005: 16 changed, 200 examined...
- 006: 7 changed, 106 examined...
- 007: 4 changed, 46 examined...
- 008: 4 changed, 19 examined...
- 009: 2 changed, 22 examined...
- 010: 2 changed, 14 examined...
- 011: 1 changed, 11 examined...
- 012: 0 changed, 7 examined...
- 157 labels changed using aseg
- 000: 103 total segments, 65 labels (332 vertices) changed
- 001: 39 total segments, 1 labels (2 vertices) changed
- 002: 38 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 71 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1394 vertices marked for relabeling...
- 1394 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 6 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 21:20:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub004 rh
- -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
- INFO: assuming MGZ format for volumes.
- using brain.finalsurfs as T1 volume...
- $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- 16676 bright wm thresholded.
- 447 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.orig...
- computing class statistics...
- border white: 249466 voxels (1.49%)
- border gray 280050 voxels (1.67%)
- WM (92.0): 93.5 +- 9.9 [70.0 --> 110.0]
- GM (76.0) : 73.7 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 45.7 (was 70)
- setting MAX_BORDER_WHITE to 114.9 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 32.5 (was 40)
- setting MAX_GRAY to 95.1 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 19.2 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 93.1, mean outside = 68.7
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.02-->5.91) (max @ vno 57288 --> 57289)
- face area 0.28 +- 0.12 (0.00-->5.12)
- mean absolute distance = 0.63 +- 0.73
- 3945 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 22 points - only 0.00% unknown
- deleting segment 2 with 16 points - only 0.00% unknown
- deleting segment 3 with 19 points - only 0.00% unknown
- deleting segment 4 with 367 points - only 0.00% unknown
- deleting segment 5 with 12 points - only 0.00% unknown
- deleting segment 6 with 19 points - only 0.00% unknown
- deleting segment 8 with 27 points - only 0.00% unknown
- deleting segment 9 with 41 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- mean border=73.5, 23 (23) missing vertices, mean dist 0.3 [0.4 (%33.2)->0.7 (%66.8))]
- %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.06-->7.18) (max @ vno 57289 --> 57288)
- face area 0.28 +- 0.13 (0.00-->4.70)
- mean absolute distance = 0.28 +- 0.44
- 2564 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7053564.0, rms=13.30
- 001: dt: 0.5000, sse=6997082.5, rms=9.513 (0.000%)
- 002: dt: 0.5000, sse=7350427.0, rms=7.360 (0.000%)
- 003: dt: 0.5000, sse=7444271.0, rms=6.004 (0.000%)
- 004: dt: 0.5000, sse=7796895.0, rms=5.239 (0.000%)
- 005: dt: 0.5000, sse=7819317.5, rms=4.831 (0.000%)
- 006: dt: 0.5000, sse=8014624.0, rms=4.629 (0.000%)
- 007: dt: 0.5000, sse=7917098.5, rms=4.520 (0.000%)
- 008: dt: 0.5000, sse=8013740.5, rms=4.453 (0.000%)
- rms = 4.42, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=7880703.0, rms=4.416 (0.000%)
- 010: dt: 0.2500, sse=5000463.5, rms=2.986 (0.000%)
- 011: dt: 0.2500, sse=4477590.5, rms=2.496 (0.000%)
- 012: dt: 0.2500, sse=4203149.5, rms=2.370 (0.000%)
- 013: dt: 0.2500, sse=4108513.5, rms=2.271 (0.000%)
- rms = 2.23, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4027308.5, rms=2.231 (0.000%)
- 015: dt: 0.1250, sse=3799791.8, rms=1.981 (0.000%)
- rms = 1.95, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=3752572.2, rms=1.949 (0.000%)
- positioning took 2.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 32 points - only 0.00% unknown
- deleting segment 3 with 17 points - only 0.00% unknown
- deleting segment 5 with 15 points - only 0.00% unknown
- deleting segment 7 with 332 points - only 0.00% unknown
- deleting segment 9 with 15 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 11 with 19 points - only 0.00% unknown
- deleting segment 12 with 21 points - only 0.00% unknown
- deleting segment 15 with 47 points - only 0.00% unknown
- deleting segment 17 with 6 points - only 0.00% unknown
- mean border=77.7, 52 (3) missing vertices, mean dist -0.2 [0.3 (%78.2)->0.2 (%21.8))]
- %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.12-->7.55) (max @ vno 57289 --> 57288)
- face area 0.35 +- 0.16 (0.00-->6.60)
- mean absolute distance = 0.20 +- 0.29
- 3193 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4647275.5, rms=5.80
- 017: dt: 0.5000, sse=4924971.5, rms=3.994 (0.000%)
- rms = 4.48, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4436095.0, rms=2.824 (0.000%)
- 019: dt: 0.2500, sse=4252136.0, rms=2.290 (0.000%)
- 020: dt: 0.2500, sse=4197376.5, rms=1.922 (0.000%)
- rms = 1.88, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4172941.0, rms=1.882 (0.000%)
- 022: dt: 0.1250, sse=4032584.2, rms=1.656 (0.000%)
- rms = 1.62, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=3988063.8, rms=1.617 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 26 points - only 0.00% unknown
- deleting segment 1 with 19 points - only 0.00% unknown
- deleting segment 2 with 19 points - only 0.00% unknown
- deleting segment 3 with 337 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 18 points - only 0.00% unknown
- deleting segment 8 with 30 points - only 0.00% unknown
- deleting segment 9 with 58 points - only 0.00% unknown
- deleting segment 10 with 11 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- deleting segment 12 with 10 points - only 0.00% unknown
- mean border=80.4, 31 (2) missing vertices, mean dist -0.1 [0.2 (%72.4)->0.2 (%27.6))]
- %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.08-->7.55) (max @ vno 57289 --> 57288)
- face area 0.34 +- 0.16 (0.00-->7.01)
- mean absolute distance = 0.17 +- 0.24
- 2593 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4254824.0, rms=3.71
- rms = 3.96, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=4120476.5, rms=2.586 (0.000%)
- 025: dt: 0.2500, sse=4094455.0, rms=1.742 (0.000%)
- 026: dt: 0.2500, sse=4122688.5, rms=1.607 (0.000%)
- 027: dt: 0.2500, sse=4139440.8, rms=1.544 (0.000%)
- rms = 1.58, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.1250, sse=4095745.0, rms=1.486 (0.000%)
- 029: dt: 0.1250, sse=4031722.5, rms=1.417 (0.000%)
- rms = 1.42, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=4031722.5, rms=1.417 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 26 points - only 0.00% unknown
- deleting segment 1 with 20 points - only 0.00% unknown
- deleting segment 2 with 20 points - only 0.00% unknown
- deleting segment 3 with 342 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 18 points - only 0.00% unknown
- deleting segment 8 with 30 points - only 0.00% unknown
- deleting segment 9 with 54 points - only 0.00% unknown
- deleting segment 10 with 11 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- deleting segment 12 with 10 points - only 0.00% unknown
- mean border=81.4, 37 (2) missing vertices, mean dist -0.0 [0.2 (%57.2)->0.2 (%42.8))]
- %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4057647.2, rms=1.82
- rms = 2.63, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=4135008.5, rms=1.240 (0.000%)
- 032: dt: 0.2500, sse=4297260.0, rms=1.055 (0.000%)
- rms = 1.06, time step reduction 2 of 3 to 0.125...
- rms = 1.05, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=4296824.5, rms=1.046 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=48.4, 45 (45) missing vertices, mean dist 1.7 [0.2 (%0.0)->2.5 (%100.0))]
- %14 local maxima, %51 large gradients and %31 min vals, 2700 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 1.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=30106472.0, rms=32.53
- 001: dt: 0.5000, sse=21591008.0, rms=26.997 (0.000%)
- 002: dt: 0.5000, sse=15619306.0, rms=22.345 (0.000%)
- 003: dt: 0.5000, sse=11606763.0, rms=18.554 (0.000%)
- 004: dt: 0.5000, sse=9140577.0, rms=15.544 (0.000%)
- 005: dt: 0.5000, sse=7668580.5, rms=13.183 (0.000%)
- 006: dt: 0.5000, sse=6802455.0, rms=11.373 (0.000%)
- 007: dt: 0.5000, sse=6300359.0, rms=9.846 (0.000%)
- 008: dt: 0.5000, sse=6045411.5, rms=8.558 (0.000%)
- 009: dt: 0.5000, sse=5964492.5, rms=7.441 (0.000%)
- 010: dt: 0.5000, sse=5982936.5, rms=6.503 (0.000%)
- 011: dt: 0.5000, sse=6048323.0, rms=5.674 (0.000%)
- 012: dt: 0.5000, sse=6169710.5, rms=5.031 (0.000%)
- 013: dt: 0.5000, sse=6338850.5, rms=4.578 (0.000%)
- 014: dt: 0.5000, sse=6460654.5, rms=4.338 (0.000%)
- 015: dt: 0.5000, sse=6585293.0, rms=4.162 (0.000%)
- 016: dt: 0.5000, sse=6653350.5, rms=4.084 (0.000%)
- 017: dt: 0.5000, sse=6681052.5, rms=3.997 (0.000%)
- rms = 3.96, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=6728599.5, rms=3.956 (0.000%)
- 019: dt: 0.2500, sse=4760715.5, rms=3.300 (0.000%)
- 020: dt: 0.2500, sse=4602831.0, rms=3.119 (0.000%)
- rms = 3.10, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4484159.0, rms=3.096 (0.000%)
- 022: dt: 0.1250, sse=4293441.0, rms=2.992 (0.000%)
- rms = 2.98, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4266689.0, rms=2.978 (0.000%)
- positioning took 2.8 minutes
- mean border=46.4, 944 (3) missing vertices, mean dist 0.1 [0.2 (%49.7)->0.6 (%50.3))]
- %31 local maxima, %39 large gradients and %25 min vals, 812 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4810111.0, rms=4.63
- 024: dt: 0.5000, sse=5095221.0, rms=3.958 (0.000%)
- rms = 3.95, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.5000, sse=6572916.5, rms=3.948 (0.000%)
- 026: dt: 0.2500, sse=4976208.5, rms=3.202 (0.000%)
- 027: dt: 0.2500, sse=5002169.0, rms=3.012 (0.000%)
- rms = 2.98, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=4876411.0, rms=2.981 (0.000%)
- 029: dt: 0.1250, sse=4719943.5, rms=2.843 (0.000%)
- rms = 2.82, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=4712444.0, rms=2.818 (0.000%)
- positioning took 0.9 minutes
- mean border=44.7, 1095 (1) missing vertices, mean dist 0.1 [0.2 (%41.7)->0.4 (%58.3))]
- %48 local maxima, %23 large gradients and %24 min vals, 958 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4897350.0, rms=3.78
- rms = 3.74, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.5000, sse=5160175.5, rms=3.737 (0.000%)
- 032: dt: 0.2500, sse=5112302.5, rms=3.034 (0.000%)
- 033: dt: 0.2500, sse=5116933.5, rms=2.870 (0.000%)
- rms = 2.87, time step reduction 2 of 3 to 0.125...
- 034: dt: 0.2500, sse=5063338.5, rms=2.865 (0.000%)
- 035: dt: 0.1250, sse=4896908.0, rms=2.699 (0.000%)
- rms = 2.68, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=4885629.5, rms=2.676 (0.000%)
- positioning took 0.7 minutes
- mean border=43.7, 2337 (1) missing vertices, mean dist 0.0 [0.2 (%47.7)->0.3 (%52.3))]
- %52 local maxima, %18 large gradients and %24 min vals, 698 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=4928219.5, rms=2.97
- rms = 3.44, time step reduction 1 of 3 to 0.250...
- 037: dt: 0.2500, sse=4827106.5, rms=2.768 (0.000%)
- 038: dt: 0.2500, sse=4997379.5, rms=2.701 (0.000%)
- rms = 2.69, time step reduction 2 of 3 to 0.125...
- 039: dt: 0.2500, sse=5080162.5, rms=2.687 (0.000%)
- 040: dt: 0.1250, sse=4980868.0, rms=2.580 (0.000%)
- rms = 2.56, time step reduction 3 of 3 to 0.062...
- 041: dt: 0.1250, sse=4995820.0, rms=2.562 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.area.pial
- vertex spacing 1.00 +- 0.42 (0.05-->8.36) (max @ vno 57289 --> 57288)
- face area 0.40 +- 0.30 (0.00-->6.47)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 134900 vertices processed
- 25000 of 134900 vertices processed
- 50000 of 134900 vertices processed
- 75000 of 134900 vertices processed
- 100000 of 134900 vertices processed
- 125000 of 134900 vertices processed
- 0 of 134900 vertices processed
- 25000 of 134900 vertices processed
- 50000 of 134900 vertices processed
- 75000 of 134900 vertices processed
- 100000 of 134900 vertices processed
- 125000 of 134900 vertices processed
- thickness calculation complete, 390:462 truncations.
- 27763 vertices at 0 distance
- 88440 vertices at 1 distance
- 87815 vertices at 2 distance
- 38143 vertices at 3 distance
- 11721 vertices at 4 distance
- 3380 vertices at 5 distance
- 963 vertices at 6 distance
- 276 vertices at 7 distance
- 85 vertices at 8 distance
- 43 vertices at 9 distance
- 20 vertices at 10 distance
- 27 vertices at 11 distance
- 22 vertices at 12 distance
- 23 vertices at 13 distance
- 17 vertices at 14 distance
- 9 vertices at 15 distance
- 10 vertices at 16 distance
- 10 vertices at 17 distance
- 6 vertices at 18 distance
- 7 vertices at 19 distance
- 16 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.thickness
- positioning took 13.3 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 21:33:35 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast rh Thu Aug 8 21:33:35 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- pctsurfcon --s sub004 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/pctsurfcon.log
- Thu Aug 8 21:33:35 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.7396/rh.wm.mgh --regheader sub004 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = rh
- ProjDist = -1
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- Done loading volume
- Computing registration from header.
- Using /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Done reading source surface
- Mapping Source Volume onto Source Subject Surface
- 1 -1 -1 -1
- using old
- Done mapping volume to surface
- Number of source voxels hit = 104673
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.7396/rh.wm.mgh
- Dim: 134900 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.7396/rh.gm.mgh --projfrac 0.3 --regheader sub004 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = rh
- ProjFrac = 0.3
- thickness = thickness
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- Done loading volume
- Computing registration from header.
- Using /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.thickness
- Done
- Mapping Source Volume onto Source Subject Surface
- 1 0.3 0.3 0.3
- using old
- Done mapping volume to surface
- Number of source voxels hit = 119229
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.7396/rh.gm.mgh
- Dim: 134900 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.7396/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/tmp.pctsurfcon.7396/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.w-g.pct.mgh
- ninputs = 2
- Checking inputs
- nframestot = 2
- Allocing output
- Done allocing
- Combining pairs
- nframes = 1
- Multiplying by 100.000000
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.w-g.pct.mgh --annot sub004 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/stats/rh.w-g.pct.stats --snr
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.w-g.pct.mgh --annot sub004 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 2000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.w-g.pct.mgh
- Vertex Area is 0.666366 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1542 1065.499
- 2 2002 caudalanteriorcingulate 1120 766.201
- 3 2003 caudalmiddlefrontal 2857 1980.405
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2049 1377.020
- 6 2006 entorhinal 482 360.414
- 7 2007 fusiform 4631 3148.177
- 8 2008 inferiorparietal 9436 6304.973
- 9 2009 inferiortemporal 5220 3490.403
- 10 2010 isthmuscingulate 1504 993.880
- 11 2011 lateraloccipital 7548 4758.041
- 12 2012 lateralorbitofrontal 3981 2628.136
- 13 2013 lingual 5046 3396.772
- 14 2014 medialorbitofrontal 2665 1770.662
- 15 2015 middletemporal 5448 3743.096
- 16 2016 parahippocampal 921 628.853
- 17 2017 paracentral 1959 1293.627
- 18 2018 parsopercularis 2236 1575.590
- 19 2019 parsorbitalis 1433 932.021
- 20 2020 parstriangularis 2465 1653.310
- 21 2021 pericalcarine 2107 1433.470
- 22 2022 postcentral 5267 3474.681
- 23 2023 posteriorcingulate 1603 1096.146
- 24 2024 precentral 6673 4302.464
- 25 2025 precuneus 5508 3661.874
- 26 2026 rostralanteriorcingulate 1057 712.167
- 27 2027 rostralmiddlefrontal 9161 6346.788
- 28 2028 superiorfrontal 9317 6268.250
- 29 2029 superiorparietal 8423 5511.184
- 30 2030 superiortemporal 5692 3698.613
- 31 2031 supramarginal 5202 3461.308
- 32 2032 frontalpole 512 346.206
- 33 2033 temporalpole 667 470.733
- 34 2034 transversetemporal 477 295.740
- 35 2035 insula 3352 2172.042
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 21:33:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub004 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Saving annotation colortable ../label/aparc.annot.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 1542 1065 2849 2.633 0.520 0.139 0.042 19 2.7 bankssts
- 1120 766 1945 2.298 0.714 0.150 0.041 21 2.0 caudalanteriorcingulate
- 2857 1980 5397 2.491 0.557 0.137 0.039 36 4.5 caudalmiddlefrontal
- 2049 1377 2937 1.952 0.448 0.175 0.067 43 5.5 cuneus
- 482 360 1609 4.028 0.640 0.155 0.055 6 1.1 entorhinal
- 4631 3148 9801 2.659 0.593 0.149 0.054 83 10.3 fusiform
- 9436 6305 16582 2.334 0.578 0.145 0.055 164 20.3 inferiorparietal
- 5220 3490 10437 2.493 0.628 0.143 0.071 150 17.7 inferiortemporal
- 1504 994 2922 2.461 0.764 0.160 0.071 38 4.3 isthmuscingulate
- 7548 4758 11186 2.163 0.464 0.160 0.085 250 23.5 lateraloccipital
- 3981 2628 8018 2.846 0.666 0.160 0.127 658 16.0 lateralorbitofrontal
- 5046 3397 7737 2.143 0.591 0.158 0.060 99 11.9 lingual
- 2665 1771 4763 2.471 0.651 0.145 0.102 107 5.2 medialorbitofrontal
- 5448 3743 13438 2.961 0.670 0.149 0.054 101 11.7 middletemporal
- 921 629 2246 3.034 0.703 0.142 0.055 16 2.2 parahippocampal
- 1959 1294 3220 2.439 0.544 0.112 0.027 16 2.2 paracentral
- 2236 1576 4442 2.572 0.628 0.120 0.035 26 3.2 parsopercularis
- 1433 932 3393 2.826 0.643 0.139 0.050 23 2.9 parsorbitalis
- 2465 1653 4788 2.576 0.468 0.132 0.037 37 3.6 parstriangularis
- 2107 1433 2376 1.768 0.420 0.144 0.057 39 4.6 pericalcarine
- 5267 3475 7978 2.058 0.779 0.121 0.034 56 7.0 postcentral
- 1603 1096 3198 2.588 0.712 0.152 0.046 28 3.0 posteriorcingulate
- 6673 4302 12211 2.577 0.565 0.126 0.099 137 16.8 precentral
- 5508 3662 9979 2.425 0.531 0.141 0.049 97 10.9 precuneus
- 1057 712 2396 2.913 0.687 0.154 0.117 45 2.4 rostralanteriorcingulate
- 9161 6347 18461 2.587 0.555 0.156 0.071 191 20.2 rostralmiddlefrontal
- 9317 6268 20621 2.911 0.540 0.132 0.042 127 16.1 superiorfrontal
- 8423 5511 12178 2.006 0.461 0.142 0.042 126 14.6 superiorparietal
- 5692 3699 12736 3.040 0.596 0.132 0.041 74 9.7 superiortemporal
- 5202 3461 9846 2.588 0.580 0.140 0.048 72 10.0 supramarginal
- 512 346 1362 2.822 0.511 0.223 0.149 29 2.9 frontalpole
- 667 471 2069 3.248 0.748 0.163 0.071 12 2.0 temporalpole
- 477 296 955 2.761 0.339 0.124 0.038 5 0.7 transversetemporal
- 3352 2172 6633 2.939 0.790 0.122 0.062 65 8.2 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 21:34:11 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub004 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs...
- reading color table from GCSA file....
- average std = 1.9 0.2 using min determinant for regularization = 0.000
- 0 singular and 851 ill-conditioned covariance matrices regularized
- input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 5 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9462 changed, 134900 examined...
- 001: 2264 changed, 36176 examined...
- 002: 713 changed, 11711 examined...
- 003: 296 changed, 4025 examined...
- 004: 149 changed, 1716 examined...
- 005: 63 changed, 845 examined...
- 006: 39 changed, 382 examined...
- 007: 28 changed, 234 examined...
- 008: 19 changed, 140 examined...
- 009: 9 changed, 101 examined...
- 010: 2 changed, 39 examined...
- 011: 4 changed, 15 examined...
- 012: 2 changed, 18 examined...
- 013: 1 changed, 9 examined...
- 014: 0 changed, 7 examined...
- 6 labels changed using aseg
- 000: 262 total segments, 178 labels (2740 vertices) changed
- 001: 101 total segments, 18 labels (156 vertices) changed
- 002: 83 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 129 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1011 vertices marked for relabeling...
- 1011 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 14 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 21:35:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub004 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
- Saving annotation colortable ../label/aparc.annot.a2009s.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 1087 740 2148 2.602 0.514 0.173 0.077 40 2.7 G_and_S_frontomargin
- 1067 699 1944 2.454 0.474 0.154 0.062 21 2.3 G_and_S_occipital_inf
- 1207 773 1947 2.168 0.636 0.125 0.066 16 2.0 G_and_S_paracentral
- 1390 950 2830 2.763 0.660 0.147 0.042 20 2.4 G_and_S_subcentral
- 1534 1076 3760 2.766 0.508 0.174 0.059 45 3.5 G_and_S_transv_frontopol
- 2953 2013 5721 2.774 0.482 0.128 0.064 59 4.8 G_and_S_cingul-Ant
- 1672 1134 3801 3.003 0.637 0.143 0.043 25 3.0 G_and_S_cingul-Mid-Ant
- 1252 870 2574 2.761 0.512 0.134 0.039 15 1.9 G_and_S_cingul-Mid-Post
- 555 354 1526 3.188 0.513 0.184 0.062 15 1.5 G_cingul-Post-dorsal
- 328 196 752 2.851 0.592 0.167 0.068 8 0.9 G_cingul-Post-ventral
- 1969 1330 2667 1.836 0.440 0.187 0.078 46 6.0 G_cuneus
- 1392 989 3309 2.565 0.673 0.142 0.049 26 2.6 G_front_inf-Opercular
- 316 208 780 2.795 0.451 0.167 0.074 10 0.7 G_front_inf-Orbital
- 1235 823 2985 2.813 0.417 0.162 0.049 26 2.6 G_front_inf-Triangul
- 3701 2596 8608 2.662 0.611 0.173 0.106 94 10.0 G_front_middle
- 5829 3899 15055 3.072 0.446 0.151 0.055 112 13.5 G_front_sup
- 477 327 1175 3.260 0.640 0.121 0.073 7 1.0 G_Ins_lg_and_S_cent_ins
- 783 487 2206 3.359 0.675 0.153 0.078 21 2.3 G_insular_short
- 2381 1520 4328 2.330 0.528 0.166 0.069 52 5.9 G_occipital_middle
- 2378 1545 3487 2.032 0.452 0.162 0.050 47 4.7 G_occipital_sup
- 1847 1222 4067 2.642 0.454 0.164 0.064 45 4.8 G_oc-temp_lat-fusifor
- 3116 2043 5130 2.142 0.639 0.169 0.068 73 8.2 G_oc-temp_med-Lingual
- 1394 973 4131 3.347 1.008 0.148 0.073 28 4.3 G_oc-temp_med-Parahip
- 3119 2054 8069 2.946 0.724 0.180 0.151 582 14.7 G_orbital
- 3746 2538 8387 2.525 0.657 0.170 0.076 100 11.7 G_pariet_inf-Angular
- 2457 1627 5379 2.679 0.576 0.148 0.057 42 5.7 G_pariet_inf-Supramar
- 2995 1944 4745 2.035 0.474 0.140 0.042 48 5.2 G_parietal_sup
- 1848 1196 3217 2.144 0.570 0.131 0.037 23 2.8 G_postcentral
- 2344 1425 5379 2.848 0.509 0.135 0.090 76 7.6 G_precentral
- 2611 1719 5874 2.545 0.566 0.164 0.063 71 6.7 G_precuneus
- 651 421 1280 2.349 0.680 0.179 0.289 79 2.0 G_rectus
- 371 232 579 2.342 0.884 0.070 0.033 3 0.4 G_subcallosal
- 393 240 858 2.912 0.411 0.121 0.037 3 0.6 G_temp_sup-G_T_transv
- 2059 1326 5981 3.192 0.575 0.154 0.052 41 4.4 G_temp_sup-Lateral
- 712 489 2026 3.513 0.575 0.116 0.034 5 0.9 G_temp_sup-Plan_polar
- 756 509 1389 2.564 0.556 0.118 0.030 8 1.0 G_temp_sup-Plan_tempo
- 2860 1901 6865 2.575 0.703 0.168 0.106 131 14.8 G_temporal_inf
- 3317 2319 9728 3.076 0.650 0.162 0.064 78 8.2 G_temporal_middle
- 484 329 784 2.391 0.489 0.103 0.021 3 0.4 Lat_Fis-ant-Horizont
- 288 192 394 2.566 0.571 0.087 0.018 1 0.2 Lat_Fis-ant-Vertical
- 1381 911 2019 2.670 0.473 0.123 0.040 11 2.1 Lat_Fis-post
- 3385 2039 4497 1.992 0.428 0.159 0.116 171 14.0 Pole_occipital
- 1930 1362 5721 3.097 0.768 0.173 0.080 45 6.9 Pole_temporal
- 3044 2111 3992 2.084 0.574 0.141 0.049 51 6.0 S_calcarine
- 2553 1704 2613 1.732 0.587 0.107 0.135 39 5.9 S_central
- 1244 813 1704 2.289 0.345 0.087 0.017 5 0.9 S_cingul-Marginalis
- 666 434 1129 2.959 0.618 0.126 0.078 88 2.0 S_circular_insula_ant
- 1298 820 1978 2.786 0.558 0.091 0.028 8 1.4 S_circular_insula_inf
- 1288 857 2008 2.810 0.356 0.110 0.027 8 1.5 S_circular_insula_sup
- 1403 960 2226 2.536 0.428 0.100 0.021 7 1.3 S_collat_transv_ant
- 592 388 766 2.077 0.378 0.153 0.057 9 1.3 S_collat_transv_post
- 2380 1633 3933 2.433 0.545 0.118 0.029 20 3.1 S_front_inf
- 2454 1696 4147 2.464 0.450 0.134 0.040 31 4.1 S_front_middle
- 2104 1430 3225 2.342 0.452 0.121 0.036 21 3.0 S_front_sup
- 384 246 381 1.801 0.362 0.109 0.024 2 0.5 S_interm_prim-Jensen
- 2346 1592 2960 1.978 0.439 0.123 0.036 21 3.4 S_intrapariet_and_P_trans
- 1172 790 1533 2.045 0.401 0.133 0.044 13 2.1 S_oc_middle_and_Lunatus
- 1490 969 2111 2.117 0.460 0.147 0.045 22 2.7 S_oc_sup_and_transversal
- 682 460 944 2.242 0.318 0.135 0.038 8 1.1 S_occipital_ant
- 789 550 1111 2.206 0.477 0.136 0.049 10 1.4 S_oc-temp_lat
- 1780 1208 2906 2.555 0.481 0.132 0.040 20 3.0 S_oc-temp_med_and_Lingual
- 575 371 779 2.279 0.447 0.106 0.042 4 0.6 S_orbital_lateral
- 682 466 908 2.287 0.704 0.128 0.045 21 1.7 S_orbital_med-olfact
- 1565 1060 2827 2.837 0.530 0.129 0.041 16 2.7 S_orbital-H_Shaped
- 1892 1249 2664 2.240 0.423 0.123 0.033 18 2.6 S_parieto_occipital
- 1582 1029 1616 1.883 0.630 0.145 0.044 29 2.4 S_pericallosal
- 2191 1456 2708 2.135 0.604 0.117 0.030 15 2.7 S_postcentral
- 1700 1152 2651 2.552 0.466 0.114 0.026 12 1.9 S_precentral-inf-part
- 1088 735 1899 2.625 0.507 0.124 0.030 9 1.5 S_precentral-sup-part
- 428 291 638 2.211 0.797 0.139 0.029 4 0.6 S_suborbital
- 1234 862 1922 2.270 0.382 0.131 0.048 16 3.0 S_subparietal
- 1505 1006 1901 2.220 0.473 0.118 0.025 12 1.7 S_temporal_inf
- 7657 5094 12052 2.531 0.604 0.130 0.038 83 11.5 S_temporal_sup
- 223 148 379 3.109 0.484 0.147 0.044 3 0.4 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 21:35:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub004 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/5.3.0/average/rh.DKTatlas40.gcs...
- reading color table from GCSA file....
- average std = 0.9 using min determinant for regularization = 0.008
- 0 singular and 237 ill-conditioned covariance matrices regularized
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 951 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2778 changed, 134900 examined...
- 001: 690 changed, 11871 examined...
- 002: 181 changed, 3754 examined...
- 003: 71 changed, 1071 examined...
- 004: 44 changed, 447 examined...
- 005: 23 changed, 269 examined...
- 006: 14 changed, 113 examined...
- 007: 5 changed, 64 examined...
- 008: 2 changed, 34 examined...
- 009: 3 changed, 16 examined...
- 010: 3 changed, 19 examined...
- 011: 2 changed, 19 examined...
- 012: 1 changed, 14 examined...
- 013: 1 changed, 7 examined...
- 014: 0 changed, 7 examined...
- 125 labels changed using aseg
- 000: 71 total segments, 38 labels (298 vertices) changed
- 001: 34 total segments, 1 labels (5 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 38 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 795 vertices marked for relabeling...
- 795 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 3 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 21:36:52 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub004 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
- Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 1174 794 2135 2.380 0.771 0.151 0.042 22 2.1 caudalanteriorcingulate
- 2890 2002 5375 2.496 0.554 0.137 0.040 36 4.6 caudalmiddlefrontal
- 2620 1738 3700 1.974 0.440 0.166 0.059 49 6.2 cuneus
- 527 389 1771 4.023 0.617 0.144 0.046 6 1.1 entorhinal
- 4007 2734 8277 2.657 0.511 0.149 0.052 69 8.3 fusiform
- 8791 5889 15299 2.318 0.589 0.145 0.053 150 18.9 inferiorparietal
- 5684 3815 11582 2.500 0.667 0.145 0.073 162 19.5 inferiortemporal
- 1586 1048 3038 2.461 0.758 0.161 0.070 39 4.5 isthmuscingulate
- 7917 4991 11642 2.151 0.468 0.157 0.082 253 24.1 lateraloccipital
- 4618 3080 9499 2.766 0.731 0.163 0.119 619 18.1 lateralorbitofrontal
- 5086 3420 7787 2.144 0.589 0.158 0.060 98 12.0 lingual
- 2051 1360 3801 2.407 0.748 0.150 0.127 105 4.4 medialorbitofrontal
- 6657 4579 15880 2.909 0.641 0.150 0.055 124 14.3 middletemporal
- 889 607 2189 3.052 0.704 0.144 0.056 15 2.2 parahippocampal
- 2022 1335 3410 2.467 0.560 0.113 0.028 16 2.3 paracentral
- 2331 1631 4576 2.581 0.619 0.122 0.036 28 3.3 parsopercularis
- 1468 955 3373 2.825 0.594 0.130 0.047 21 2.8 parsorbitalis
- 2611 1768 5112 2.572 0.474 0.136 0.042 42 4.1 parstriangularis
- 2123 1445 2386 1.763 0.422 0.144 0.057 39 4.7 pericalcarine
- 5722 3769 8691 2.091 0.777 0.122 0.034 62 7.8 postcentral
- 1664 1132 3275 2.583 0.703 0.150 0.045 28 3.0 posteriorcingulate
- 6545 4222 12004 2.569 0.569 0.127 0.101 137 16.6 precentral
- 5574 3711 10148 2.410 0.533 0.141 0.049 100 10.9 precuneus
- 1139 767 2517 2.959 0.592 0.155 0.113 46 2.7 rostralanteriorcingulate
- 5898 4045 11640 2.559 0.593 0.155 0.078 117 13.1 rostralmiddlefrontal
- 12814 8698 27725 2.829 0.534 0.138 0.046 200 24.2 superiorfrontal
- 7151 4688 10434 2.013 0.463 0.141 0.042 106 12.3 superiorparietal
- 7495 4930 17012 3.020 0.629 0.137 0.047 106 14.9 superiortemporal
- 4943 3269 9179 2.531 0.557 0.140 0.047 70 9.6 supramarginal
- 457 285 924 2.754 0.339 0.124 0.038 4 0.7 transversetemporal
- 3107 2023 6326 3.046 0.641 0.126 0.061 125 6.8 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 21:37:12 CEST 2013
- bbregister --s sub004 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat.log
- Thu Aug 8 21:37:12 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub004 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.lta --init-fsl --T2
- $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996814, 0.0369416, 0.0706971)
- j_ras = (0.0317143, 0.996777, -0.0736842)
- k_ras = (0.0731912, 0.0712073, 0.994773)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii...
- fslregister --s sub004 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fslregister.log
- Thu Aug 8 21:37:17 CEST 2013
- --s sub004 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister --dof 6 --fsvol brainmask.mgz
- $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
- snake5
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- nIters 1
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -5.58794e-09, -7.45058e-09)
- j_ras = (7.45058e-09, 1.49012e-08, -1)
- k_ras = (-1.86265e-09, 1, 7.45058e-09)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii --frame 0
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996814, 0.0369416, 0.0706971)
- j_ras = (0.0317143, 0.996777, -0.0736842)
- k_ras = (0.0731912, 0.0712073, 0.994773)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311089
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/reg0.7795.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fsl.mat0 --s sub004 --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- INFO: no target volume specified, assuming FreeSurfer orig volume.
- target volume orig
- movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/reg0.7795.dat
- LoadVol 0
- ZeroCRAS 0
- $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
- Diagnostic Level -1
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz
- Ttarg: --------------------
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.893;
- 0.000 0.000 0.667 -128.000;
- 0.000 -0.667 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- mkheaderreg = 1, float2int = 0
- Computing reg from header (and possibly input matrix)
- ---- Input registration matrix (computed) --------
- 0.997 -0.037 -0.071 0.000;
- 0.073 0.071 0.995 -0.000;
- -0.032 -0.997 0.074 -0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.997 -0.037 -0.071 0.000;
- 0.073 0.071 0.995 -0.000;
- -0.032 -0.997 0.074 -0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub004
- RegMat ---------------------------
- 0.997 -0.037 -0.071 0.000;
- 0.073 0.071 0.995 -0.000;
- -0.032 -0.997 0.074 -0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311089, ref det = -1
- Thu Aug 8 21:37:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fsl.mat0
- Thu Aug 8 21:41:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub004 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.997 -0.029 -0.076 45.787;
- -0.074 0.070 -0.995 254.922;
- 0.034 0.997 0.067 -11.324;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- INFO: no target volume specified, assuming FreeSurfer orig volume.
- target volume orig
- movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat
- LoadVol 0
- ZeroCRAS 0
- $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
- Diagnostic Level -1
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz
- Ttarg: --------------------
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.893;
- 0.000 0.000 0.667 -128.000;
- 0.000 -0.667 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- mkheaderreg = 0, float2int = 0
- FSLOUTPUTTYPE NIFTI
- fsl2TkReg: mov det = -0.311089, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.997 -0.034 -0.074 -0.150;
- 0.076 0.067 0.995 1.396;
- -0.029 -0.997 0.070 0.282;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.997 -0.034 -0.074 -0.150;
- 0.076 0.067 0.995 1.396;
- -0.029 -0.997 0.070 0.282;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub004
- RegMat ---------------------------
- 0.997 -0.034 -0.074 -0.150;
- 0.076 0.067 0.995 1.396;
- -0.029 -0.997 0.070 0.282;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 21:37:17 CEST 2013
- Ended at Thu Aug 8 21:48:03 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
- $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat
- subject sub004
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat
- UseMask 0
- UseLH 1
- UseRH 1
- nsubsamp 100
- PenaltySign -1
- PenaltySlope 0.500000
- PenaltyCenter 0.000000
- surfname white
- GMProjFrac 0.500000
- WMProjAbs 2.000000
- lhcostfile (null)
- rhcostfile (null)
- interp trilinear (1)
- frame 0
- TolPowell 0.000100
- nMaxItersPowell 36
- n1dmin 3
- Profile 0
- Gdiag_no -1
- AddNoise 0 (0)
- SynthSeed 1376763169
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.997 -0.034 -0.074 -0.150;
- 0.076 0.067 0.995 1.396;
- -0.029 -0.997 0.070 0.282;
- 0.000 0.000 0.000 1.000;
- Loading mov
- Projecting LH Surfs
- Loading lh.white surf
- Loading lh.thickness for GM
- GM Proj: 1 0.500000 2.000000
- WM Proj: 0 0.500000 2.000000
- Projecting RH Surfs
- Loading rh.white surf
- Loading rh.thickness
- Projecting RH Surfs
- Computing relative cost
- 0 -25.0 -25.0 -25.0 0.990335
- 1 -25.0 -25.0 25.0 1.046258
- 2 -25.0 25.0 -25.0 1.034979
- 3 -25.0 25.0 25.0 1.009670
- 4 25.0 -25.0 -25.0 1.002974
- 5 25.0 -25.0 25.0 0.984347
- 6 25.0 25.0 -25.0 1.026177
- 7 25.0 25.0 25.0 0.983004
- REL: 8 0.395479 8.077746 1.009718 rel = 0.391672
- Initial costs ----------------
- Number of surface hits 2556
- WM Intensity 63.9983 +/- 10.9597
- Ctx Intensity 77.7737 +/- 15.9144
- Pct Contrast 18.6680 +/- 22.7255
- Cost 0.3955
- RelCost 0.3917
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9607 0.9607 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9091 0.9091 0.0
- 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.8647 0.8647 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8209 0.8209 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7859 0.7859 0.0
- 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7537 0.7537 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6957 0.6957 0.0
- 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6039 0.6039 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3955 0.3955 0.0
- Brute Force --------------------------
- Min cost was 0.395479
- Number of iterations 729
- Search time 2.737000 sec
- Parameters at best (transmm, rotdeg)
- 0.000 0.000 0.000 0.000 0.000 0.000
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 0
- 1 0
- 2 0
- 3 0
- 4 0
- 5 0
- 10 0.007 0.000 0.000 0.000 0.000 0.000 0.3954699444
- 12 0.005 0.000 0.000 0.000 0.000 0.000 0.3954657001
- 13 0.004 0.000 0.000 0.000 0.000 0.000 0.3954656519
- 17 0.004 -1.618 0.000 0.000 0.000 0.000 0.1426153987
- 24 0.004 -1.616 0.000 0.000 0.000 0.000 0.1426134406
- 25 0.004 -1.613 0.000 0.000 0.000 0.000 0.1426091991
- 34 0.004 -1.613 0.382 0.000 0.000 0.000 0.1302286759
- 36 0.004 -1.613 0.268 0.000 0.000 0.000 0.1286964379
- 38 0.004 -1.613 0.303 0.000 0.000 0.000 0.1284859533
- 39 0.004 -1.613 0.297 0.000 0.000 0.000 0.1284730009
- 40 0.004 -1.613 0.296 0.000 0.000 0.000 0.1284716918
- 47 0.004 -1.613 0.296 0.382 0.000 0.000 0.0992088363
- 48 0.004 -1.613 0.296 0.450 0.000 0.000 0.0980428336
- 49 0.004 -1.613 0.296 0.481 0.000 0.000 0.0976778180
- 52 0.004 -1.613 0.296 0.521 0.000 0.000 0.0976072447
- 53 0.004 -1.613 0.296 0.507 0.000 0.000 0.0974022707
- 55 0.004 -1.613 0.296 0.505 0.000 0.000 0.0973990432
- 65 0.004 -1.613 0.296 0.505 -0.007 0.000 0.0973140773
- 66 0.004 -1.613 0.296 0.505 -0.023 0.000 0.0972947579
- 68 0.004 -1.613 0.296 0.505 -0.016 0.000 0.0972744908
- 77 0.004 -1.613 0.296 0.505 -0.016 0.031 0.0969850361
- 79 0.004 -1.613 0.296 0.505 -0.016 0.034 0.0969796928
- 91 0.015 -1.613 0.296 0.505 -0.016 0.034 0.0969708019
- 92 0.011 -1.613 0.296 0.505 -0.016 0.034 0.0969688010
- 93 0.010 -1.613 0.296 0.505 -0.016 0.034 0.0969678084
- 95 0.009 -1.613 0.296 0.505 -0.016 0.034 0.0969673702
- 102 0.009 -1.583 0.296 0.505 -0.016 0.034 0.0957225221
- 103 0.009 -1.512 0.296 0.505 -0.016 0.034 0.0956431997
- 105 0.009 -1.546 0.296 0.505 -0.016 0.034 0.0951402153
- 106 0.009 -1.547 0.296 0.505 -0.016 0.034 0.0951385373
- 107 0.009 -1.549 0.296 0.505 -0.016 0.034 0.0951360701
- 110 0.009 -1.550 0.296 0.505 -0.016 0.034 0.0951357010
- 118 0.009 -1.550 0.012 0.505 -0.016 0.034 0.0873739917
- 119 0.009 -1.550 0.018 0.505 -0.016 0.034 0.0873375201
- 120 0.009 -1.550 0.040 0.505 -0.016 0.034 0.0872135720
- 121 0.009 -1.550 0.138 0.505 -0.016 0.034 0.0862267258
- 125 0.009 -1.550 0.125 0.505 -0.016 0.034 0.0861260298
- 126 0.009 -1.550 0.124 0.505 -0.016 0.034 0.0861259001
- 135 0.009 -1.550 0.124 0.566 -0.016 0.034 0.0858010437
- 137 0.009 -1.550 0.124 0.541 -0.016 0.034 0.0855510203
- 139 0.009 -1.550 0.124 0.532 -0.016 0.034 0.0855427346
- 141 0.009 -1.550 0.124 0.535 -0.016 0.034 0.0855387127
- 151 0.009 -1.550 0.124 0.535 -0.019 0.034 0.0855114469
- 152 0.009 -1.550 0.124 0.535 -0.034 0.034 0.0854628992
- 154 0.009 -1.550 0.124 0.535 -0.030 0.034 0.0854598576
- 156 0.009 -1.550 0.124 0.535 -0.029 0.034 0.0854598167
- 165 0.009 -1.550 0.124 0.535 -0.029 0.049 0.0851642324
- 166 0.009 -1.550 0.124 0.535 -0.029 0.102 0.0849879596
- 168 0.009 -1.550 0.124 0.535 -0.029 0.082 0.0848723293
- 169 0.009 -1.550 0.124 0.535 -0.029 0.081 0.0848697572
- 172 0.009 -1.550 0.124 0.535 -0.029 0.080 0.0848696467
- 173 0.015 -1.486 -0.049 0.565 -0.042 0.126 0.0833334988
- 180 0.014 -1.496 -0.020 0.560 -0.040 0.118 0.0832923721
- 181 0.014 -1.495 -0.024 0.561 -0.040 0.120 0.0832759040
- 182 0.015 -1.492 -0.031 0.562 -0.040 0.121 0.0832675161
- 183 0.015 -1.493 -0.030 0.562 -0.040 0.121 0.0832667772
- 184 0.015 -1.493 -0.029 0.562 -0.040 0.121 0.0832663080
- 185 0.015 -1.493 -0.029 0.562 -0.040 0.121 0.0832662665
- 187 0.015 -1.493 -0.029 0.562 -0.040 0.121 0.0832661555
- 189 0.015 -1.493 -0.029 0.562 -0.040 0.121 0.0832661057
- 197 0.196 -1.493 -0.029 0.562 -0.040 0.121 0.0829808860
- 198 0.152 -1.493 -0.029 0.562 -0.040 0.121 0.0820850604
- 199 0.110 -1.493 -0.029 0.562 -0.040 0.121 0.0817788489
- 200 0.108 -1.493 -0.029 0.562 -0.040 0.121 0.0817786502
- 202 0.109 -1.493 -0.029 0.562 -0.040 0.121 0.0817783720
- 210 0.109 -1.487 -0.029 0.562 -0.040 0.121 0.0817533131
- 213 0.109 -1.486 -0.029 0.562 -0.040 0.121 0.0817527766
- 220 0.109 -1.486 -0.029 0.562 -0.040 0.113 0.0817381302
- 222 0.109 -1.486 -0.029 0.562 -0.040 0.114 0.0817377352
- 230 0.109 -1.486 -0.029 0.623 -0.040 0.114 0.0788986594
- 231 0.109 -1.486 -0.029 0.675 -0.040 0.114 0.0788313512
- 232 0.109 -1.486 -0.029 0.650 -0.040 0.114 0.0786353742
- 234 0.109 -1.486 -0.029 0.649 -0.040 0.114 0.0786323986
- 236 0.109 -1.486 -0.029 0.645 -0.040 0.114 0.0786236453
- 248 0.109 -1.486 -0.029 0.645 -0.045 0.114 0.0786126261
- 251 0.109 -1.486 -0.029 0.645 -0.046 0.114 0.0786115614
- 258 0.111 -1.462 -0.095 0.657 -0.050 0.131 0.0776070620
- 259 0.111 -1.462 -0.093 0.656 -0.050 0.131 0.0775988412
- 260 0.110 -1.465 -0.085 0.655 -0.050 0.129 0.0775621260
- 263 0.110 -1.466 -0.082 0.654 -0.050 0.128 0.0775605046
- 266 0.110 -1.466 -0.083 0.654 -0.050 0.128 0.0775604261
- 268 0.211 -1.382 -0.289 0.774 -0.070 0.177 0.0766942562
- 274 0.173 -1.414 -0.210 0.728 -0.062 0.158 0.0762590916
- 275 0.187 -1.403 -0.239 0.745 -0.065 0.165 0.0760664021
- 277 0.196 -1.395 -0.258 0.756 -0.067 0.169 0.0759852322
- 279 0.194 -1.397 -0.253 0.753 -0.066 0.168 0.0759797410
- 281 0.195 -1.396 -0.255 0.754 -0.067 0.169 0.0759778584
- 293 0.168 -1.396 -0.255 0.754 -0.067 0.169 0.0758012494
- 294 0.167 -1.396 -0.255 0.754 -0.067 0.169 0.0757999063
- 295 0.164 -1.396 -0.255 0.754 -0.067 0.169 0.0757958398
- 298 0.163 -1.396 -0.255 0.754 -0.067 0.169 0.0757955273
- 308 0.163 -1.373 -0.255 0.754 -0.067 0.169 0.0756043267
- 311 0.163 -1.374 -0.255 0.754 -0.067 0.169 0.0756019237
- 321 0.163 -1.374 -0.255 0.754 -0.067 0.164 0.0756000897
- 323 0.163 -1.374 -0.255 0.754 -0.067 0.166 0.0755996286
- 329 0.159 -1.414 -0.149 0.735 -0.059 0.137 0.0746940753
- 333 0.159 -1.411 -0.155 0.737 -0.059 0.139 0.0746885499
- 334 0.159 -1.412 -0.153 0.736 -0.059 0.139 0.0746843485
- 335 0.159 -1.412 -0.153 0.736 -0.059 0.138 0.0746830986
- 337 0.159 -1.412 -0.152 0.736 -0.059 0.138 0.0746830979
- 339 0.159 -1.412 -0.152 0.736 -0.059 0.138 0.0746829520
- 347 0.159 -1.412 -0.152 0.736 -0.060 0.138 0.0746743997
- 348 0.159 -1.412 -0.152 0.736 -0.072 0.138 0.0746272444
- 350 0.159 -1.412 -0.152 0.736 -0.071 0.138 0.0746269633
- 363 0.160 -1.412 -0.154 0.737 -0.071 0.139 0.0746260905
- 376 0.139 -1.412 -0.154 0.737 -0.071 0.139 0.0744794309
- 387 0.139 -1.398 -0.154 0.737 -0.071 0.139 0.0743690639
- 397 0.139 -1.398 -0.154 0.737 -0.071 0.208 0.0743571635
- 399 0.139 -1.398 -0.154 0.737 -0.071 0.173 0.0739818935
- 402 0.139 -1.398 -0.154 0.737 -0.071 0.167 0.0739658896
- 411 0.139 -1.402 -0.141 0.735 -0.070 0.164 0.0737362309
- 413 0.138 -1.408 -0.126 0.732 -0.069 0.159 0.0736378142
- 414 0.138 -1.408 -0.126 0.732 -0.069 0.159 0.0736375626
- 427 0.138 -1.408 -0.126 0.732 -0.071 0.159 0.0736364869
- 430 0.138 -1.408 -0.126 0.732 -0.070 0.159 0.0736363646
- 436 0.177 -1.376 -0.205 0.778 -0.078 0.178 0.0735789822
- 437 0.159 -1.391 -0.168 0.756 -0.075 0.169 0.0734949224
- 439 0.151 -1.398 -0.152 0.747 -0.073 0.165 0.0734198939
- 441 0.151 -1.397 -0.152 0.747 -0.073 0.165 0.0734197493
- 445 0.142 -1.383 -0.150 0.757 -0.075 0.192 0.0733829947
- 477 0.153 -1.397 -0.152 0.747 -0.073 0.185 0.0733214881
- 478 0.153 -1.397 -0.152 0.747 -0.073 0.183 0.0733108810
- 479 0.153 -1.397 -0.152 0.747 -0.073 0.180 0.0733066595
- 488 0.152 -1.400 -0.145 0.746 -0.073 0.178 0.0732080094
- 490 0.152 -1.405 -0.131 0.743 -0.072 0.175 0.0731436851
- 506 0.152 -1.405 -0.131 0.743 -0.073 0.175 0.0731431375
- 507 0.152 -1.405 -0.131 0.743 -0.074 0.175 0.0731430000
- 516 0.167 -1.393 -0.161 0.761 -0.077 0.182 0.0730938107
- 517 0.163 -1.396 -0.154 0.757 -0.076 0.180 0.0730515959
- 518 0.161 -1.398 -0.149 0.754 -0.075 0.179 0.0730406343
- 519 0.160 -1.398 -0.148 0.753 -0.075 0.179 0.0730405229
- 525 0.169 -1.399 -0.144 0.759 -0.077 0.192 0.0728348192
- 530 0.175 -1.399 -0.142 0.763 -0.079 0.200 0.0727927115
- 532 0.176 -1.400 -0.142 0.764 -0.079 0.202 0.0727911080
- 535 0.176 -1.400 -0.142 0.764 -0.079 0.201 0.0727911058
- 536 0.176 -1.400 -0.142 0.764 -0.079 0.202 0.0727909245
- 537 0.176 -1.400 -0.142 0.764 -0.079 0.202 0.0727909004
- 559 0.176 -1.387 -0.142 0.764 -0.079 0.202 0.0727378480
- 560 0.176 -1.389 -0.142 0.764 -0.079 0.202 0.0727336464
- 561 0.176 -1.390 -0.142 0.764 -0.079 0.202 0.0727304348
- 563 0.176 -1.391 -0.142 0.764 -0.079 0.202 0.0727302022
- 584 0.173 -1.394 -0.135 0.760 -0.078 0.200 0.0727220625
- 586 0.173 -1.394 -0.136 0.761 -0.078 0.200 0.0727217494
- 606 0.177 -1.394 -0.134 0.763 -0.079 0.205 0.0727162184
- 607 0.176 -1.394 -0.135 0.762 -0.079 0.204 0.0727155011
- 608 0.176 -1.394 -0.135 0.762 -0.079 0.204 0.0727154412
- 611 0.176 -1.394 -0.135 0.762 -0.079 0.204 0.0727154173
- 612 0.176 -1.394 -0.135 0.762 -0.079 0.204 0.0727153439
- 625 0.177 -1.394 -0.135 0.762 -0.079 0.204 0.0727145586
- 636 0.177 -1.392 -0.135 0.762 -0.079 0.204 0.0727101900
- 648 0.177 -1.392 -0.135 0.762 -0.079 0.203 0.0727091493
- 657 0.176 -1.392 -0.133 0.762 -0.079 0.202 0.0727083412
- 670 0.176 -1.392 -0.133 0.762 -0.081 0.202 0.0727072398
- 678 0.178 -1.393 -0.133 0.762 -0.081 0.204 0.0727063435
- 685 0.179 -1.391 -0.131 0.763 -0.083 0.204 0.0727007357
- 690 0.180 -1.390 -0.130 0.763 -0.084 0.204 0.0727005768
- 692 0.180 -1.391 -0.130 0.763 -0.084 0.204 0.0727003955
- 693 0.180 -1.391 -0.130 0.763 -0.083 0.204 0.0727003020
- 711 0.178 -1.391 -0.130 0.763 -0.083 0.204 0.0726993645
- 719 0.180 -1.391 -0.130 0.764 -0.084 0.207 0.0726991298
- 720 0.179 -1.391 -0.130 0.763 -0.084 0.206 0.0726990916
- 723 0.179 -1.391 -0.130 0.763 -0.084 0.206 0.0726990741
- 725 0.179 -1.391 -0.130 0.763 -0.084 0.206 0.0726990063
- 737 0.179 -1.391 -0.130 0.763 -0.084 0.205 0.0726982144
- 749 0.177 -1.393 -0.126 0.761 -0.083 0.204 0.0726891825
- 753 0.176 -1.393 -0.124 0.760 -0.083 0.204 0.0726887712
- 754 0.177 -1.393 -0.125 0.760 -0.083 0.204 0.0726887335
- 755 0.177 -1.393 -0.125 0.760 -0.083 0.204 0.0726887232
- 768 0.178 -1.392 -0.123 0.760 -0.085 0.204 0.0726861836
- 772 0.178 -1.392 -0.124 0.760 -0.084 0.204 0.0726861621
- 773 0.178 -1.392 -0.123 0.760 -0.085 0.204 0.0726861545
- 775 0.178 -1.392 -0.123 0.760 -0.085 0.204 0.0726861539
- 776 0.178 -1.392 -0.123 0.760 -0.085 0.204 0.0726860383
- 784 0.178 -1.392 -0.123 0.760 -0.085 0.204 0.0726860034
- 810 0.178 -1.392 -0.123 0.760 -0.085 0.204 0.0726859213
- 821 0.178 -1.392 -0.123 0.760 -0.085 0.208 0.0726852144
- 822 0.178 -1.392 -0.123 0.760 -0.085 0.206 0.0726851212
- 824 0.178 -1.392 -0.123 0.760 -0.085 0.207 0.0726847545
- 834 0.177 -1.392 -0.122 0.760 -0.085 0.207 0.0726839707
- 855 0.178 -1.392 -0.121 0.760 -0.085 0.207 0.0726838584
- 857 0.178 -1.392 -0.121 0.760 -0.085 0.207 0.0726838037
- 860 0.178 -1.392 -0.121 0.760 -0.085 0.207 0.0726837988
- 861 0.178 -1.392 -0.121 0.760 -0.085 0.207 0.0726837969
- 863 0.178 -1.392 -0.121 0.760 -0.085 0.207 0.0726836686
- Powell done niters = 9
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.006857
- 1 -25.0 -25.0 25.0 1.044254
- 2 -25.0 25.0 -25.0 1.029143
- 3 -25.0 25.0 25.0 1.002896
- 4 25.0 -25.0 -25.0 0.978538
- 5 25.0 -25.0 25.0 1.013653
- 6 25.0 25.0 -25.0 1.040085
- 7 25.0 25.0 25.0 0.996926
- REL: 8 0.072684 8.112353 1.014044 rel = 0.071677
- Number of iterations 9
- Min cost was 0.072684
- Number of FunctionCalls 867
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 3.235000 sec
- Parameters at optimum (transmm) 0.17782 -1.39207 -0.12115
- Parameters at optimum (rotdeg) 0.75960 -0.08518 0.20712
- Final costs ----------------
- Number of surface hits 2556
- WM Intensity 61.8206 +/- 9.0689
- Ctx Intensity 78.7208 +/- 9.5066
- Pct Contrast 24.2141 +/- 13.9696
- Cost 0.0727
- RelCost 0.3917
- Reg at min cost was
- 0.996 -0.033 -0.078 0.022;
- 0.080 0.081 0.994 -0.000;
- -0.026 -0.996 0.083 0.179;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat, type = 14
- Original Reg
- 0.997 -0.034 -0.074 -0.150;
- 0.076 0.067 0.995 1.396;
- -0.029 -0.997 0.070 0.282;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.001 0.004 -0.172;
- -0.004 -0.013 0.001 1.396;
- -0.002 -0.001 -0.013 0.103;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.774158
- Computing change in rh position
- Surface RMS Diff (mm) 1.670984 2.632894
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat
- subject sub004
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat
- UseMask 0
- UseLH 1
- UseRH 1
- nsubsamp 1
- PenaltySign -1
- PenaltySlope 0.500000
- PenaltyCenter 0.000000
- surfname white
- GMProjFrac 0.500000
- WMProjAbs 2.000000
- lhcostfile (null)
- rhcostfile (null)
- interp trilinear (1)
- frame 0
- TolPowell 0.000000
- nMaxItersPowell 36
- n1dmin 3
- Profile 0
- Gdiag_no -1
- AddNoise 0 (0)
- SynthSeed 1376849299
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.996 -0.033 -0.078 0.022;
- 0.080 0.081 0.994 -0.000;
- -0.026 -0.996 0.083 0.179;
- 0.000 0.000 0.000 1.000;
- Loading mov
- Projecting LH Surfs
- Loading lh.white surf
- Loading lh.thickness for GM
- GM Proj: 1 0.500000 2.000000
- WM Proj: 0 0.500000 2.000000
- Projecting RH Surfs
- Loading rh.white surf
- Loading rh.thickness
- Projecting RH Surfs
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.004646
- 1 -25.0 -25.0 25.0 1.013329
- 2 -25.0 25.0 -25.0 1.015470
- 3 -25.0 25.0 25.0 0.997744
- 4 25.0 -25.0 -25.0 1.012491
- 5 25.0 -25.0 25.0 1.013753
- 6 25.0 25.0 -25.0 1.013924
- 7 25.0 25.0 25.0 1.007717
- REL: 8 0.095373 8.079073 1.009884 rel = 0.0944391
- Initial costs ----------------
- Number of surface hits 254571
- WM Intensity 61.9760 +/- 9.7096
- Ctx Intensity 78.5671 +/- 9.7566
- Pct Contrast 23.8049 +/- 14.7579
- Cost 0.0954
- RelCost 0.0944
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0866 0.0866 0.0
- 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0865 0.0865 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0829 0.0829 0.0
- 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0824 0.0824 0.0
- 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0822 0.0822 0.0
- 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0815 0.0815 0.0
- 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0793 0.0793 0.0
- 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0791 0.0791 0.0
- 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0785 0.0785 0.0
- 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.0765 0.0765 0.0
- 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0762 0.0762 0.0
- 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0757 0.0757 0.0
- 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0755 0.0755 0.0
- 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0747 0.0747 0.0
- 346 0.0000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.0744 0.0744 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0727 0.0727 0.0
- Brute Force --------------------------
- Min cost was 0.072684
- Number of iterations 729
- Search time 2.098000 sec
- Parameters at best (transmm, rotdeg)
- 0.000 0.000 0.000 0.000 0.000 0.000
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 0
- 1 0
- 2 0
- 3 0
- 4 0
- 5 0
- 7 0.165 0.000 0.000 0.000 0.000 0.000 0.0933845584
- 9 0.167 0.000 0.000 0.000 0.000 0.000 0.0933841782
- 12 0.168 0.000 0.000 0.000 0.000 0.000 0.0933841401
- 19 0.168 -0.054 0.000 0.000 0.000 0.000 0.0930159749
- 20 0.168 -0.059 0.000 0.000 0.000 0.000 0.0930000867
- 21 0.168 -0.080 0.000 0.000 0.000 0.000 0.0929866965
- 23 0.168 -0.073 0.000 0.000 0.000 0.000 0.0929812374
- 32 0.168 -0.073 -0.109 0.000 0.000 0.000 0.0913775735
- 33 0.168 -0.073 -0.139 0.000 0.000 0.000 0.0912598531
- 34 0.168 -0.073 -0.149 0.000 0.000 0.000 0.0912557191
- 35 0.168 -0.073 -0.146 0.000 0.000 0.000 0.0912541483
- 36 0.168 -0.073 -0.145 0.000 0.000 0.000 0.0912541193
- 45 0.168 -0.073 -0.145 -0.009 0.000 0.000 0.0912387253
- 46 0.168 -0.073 -0.145 -0.011 0.000 0.000 0.0912383717
- 48 0.168 -0.073 -0.145 -0.010 0.000 0.000 0.0912383515
- 55 0.168 -0.073 -0.145 -0.010 -0.057 0.000 0.0907298276
- 56 0.168 -0.073 -0.145 -0.010 -0.075 0.000 0.0906906176
- 66 0.168 -0.073 -0.145 -0.010 -0.075 -0.008 0.0906491432
- 67 0.168 -0.073 -0.145 -0.010 -0.075 -0.034 0.0905906757
- 68 0.168 -0.073 -0.145 -0.010 -0.075 -0.033 0.0905904571
- 77 0.150 -0.073 -0.145 -0.010 -0.075 -0.033 0.0905518435
- 89 0.150 -0.046 -0.145 -0.010 -0.075 -0.033 0.0904328796
- 90 0.150 -0.041 -0.145 -0.010 -0.075 -0.033 0.0904259436
- 91 0.150 -0.035 -0.145 -0.010 -0.075 -0.033 0.0904249695
- 92 0.150 -0.037 -0.145 -0.010 -0.075 -0.033 0.0904248135
- 101 0.150 -0.037 -0.143 -0.010 -0.075 -0.033 0.0904206539
- 102 0.150 -0.037 -0.136 -0.010 -0.075 -0.033 0.0904164606
- 104 0.150 -0.037 -0.138 -0.010 -0.075 -0.033 0.0904164075
- 113 0.150 -0.037 -0.138 -0.006 -0.075 -0.033 0.0904161406
- 114 0.150 -0.037 -0.138 -0.008 -0.075 -0.033 0.0904158820
- 124 0.150 -0.037 -0.138 -0.008 -0.074 -0.033 0.0904157128
- 133 0.150 -0.037 -0.138 -0.008 -0.074 -0.041 0.0904108071
- 134 0.150 -0.037 -0.138 -0.008 -0.074 -0.040 0.0904104333
- 143 0.146 -0.037 -0.138 -0.008 -0.074 -0.040 0.0904069638
- 144 0.142 -0.037 -0.138 -0.008 -0.074 -0.040 0.0904052471
- 164 0.142 -0.037 -0.139 -0.008 -0.074 -0.040 0.0904049513
- 165 0.142 -0.037 -0.140 -0.008 -0.074 -0.040 0.0904048650
- 186 0.142 -0.037 -0.140 -0.008 -0.073 -0.040 0.0904047886
- 195 0.142 -0.037 -0.140 -0.008 -0.073 -0.045 0.0904041077
- 196 0.142 -0.037 -0.140 -0.008 -0.073 -0.043 0.0904037585
- 204 0.139 -0.037 -0.140 -0.008 -0.072 -0.044 0.0904032972
- 205 0.140 -0.037 -0.140 -0.008 -0.072 -0.044 0.0904032652
- 206 0.140 -0.037 -0.140 -0.008 -0.072 -0.044 0.0904032466
- 241 0.140 -0.037 -0.139 -0.008 -0.072 -0.044 0.0904031320
- 261 0.140 -0.037 -0.139 -0.008 -0.073 -0.044 0.0904030116
- 269 0.140 -0.037 -0.139 -0.008 -0.073 -0.044 0.0904030093
- 271 0.140 -0.037 -0.139 -0.008 -0.073 -0.044 0.0904029927
- 273 0.140 -0.037 -0.139 -0.008 -0.073 -0.044 0.0904029889
- 274 0.140 -0.037 -0.139 -0.008 -0.073 -0.044 0.0904029708
- 285 0.140 -0.037 -0.139 -0.008 -0.073 -0.045 0.0904029541
- 293 0.140 -0.038 -0.139 -0.008 -0.073 -0.045 0.0904029459
- 313 0.140 -0.038 -0.139 -0.007 -0.073 -0.045 0.0904029052
- 329 0.139 -0.038 -0.139 -0.007 -0.073 -0.045 0.0904028744
- 332 0.139 -0.038 -0.139 -0.007 -0.073 -0.045 0.0904028657
- 333 0.139 -0.038 -0.139 -0.007 -0.073 -0.045 0.0904028591
- 365 0.139 -0.038 -0.140 -0.007 -0.073 -0.045 0.0904028467
- 393 0.140 -0.038 -0.140 -0.007 -0.073 -0.045 0.0904028205
- 401 0.140 -0.038 -0.140 -0.007 -0.073 -0.045 0.0904028168
- 456 0.140 -0.038 -0.140 -0.007 -0.073 -0.045 0.0904027985
- Powell done niters = 7
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.003687
- 1 -25.0 -25.0 25.0 1.010969
- 2 -25.0 25.0 -25.0 1.015503
- 3 -25.0 25.0 25.0 0.996017
- 4 25.0 -25.0 -25.0 1.011593
- 5 25.0 -25.0 25.0 1.012373
- 6 25.0 25.0 -25.0 1.013332
- 7 25.0 25.0 25.0 1.008502
- REL: 8 0.090403 8.071978 1.008997 rel = 0.0895967
- Number of iterations 7
- Min cost was 0.090403
- Number of FunctionCalls 525
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 63.518000 sec
- Parameters at optimum (transmm) 0.13977 -0.03823 -0.14024
- Parameters at optimum (rotdeg) -0.00674 -0.07340 -0.04490
- Final costs ----------------
- Number of surface hits 254571
- WM Intensity 61.9785 +/- 9.7235
- Ctx Intensity 78.5620 +/- 9.7033
- Pct Contrast 23.8028 +/- 14.6897
- Cost 0.0904
- RelCost 0.0944
- Reg at min cost was
- 0.997 -0.031 -0.077 0.162;
- 0.079 0.080 0.994 -0.039;
- -0.025 -0.996 0.083 0.039;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.996 -0.033 -0.078 0.022;
- 0.080 0.081 0.994 -0.000;
- -0.026 -0.996 0.083 0.179;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 -0.001 -0.001 -0.140;
- 0.001 0.000 -0.000 0.038;
- -0.001 0.000 0.000 0.140;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.238989
- Computing change in rh position
- Surface RMS Diff (mm) 0.221031 0.321591
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.lta
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- INFO: no target volume specified, assuming FreeSurfer orig volume.
- target volume orig
- movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat
- LoadVol 0
- ZeroCRAS 0
- $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
- Diagnostic Level -1
- ---- Input registration matrix --------
- 0.997 -0.031 -0.077 0.162;
- 0.079 0.080 0.994 -0.039;
- -0.025 -0.996 0.083 0.039;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz
- Ttarg: --------------------
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.893;
- 0.000 0.000 0.667 -128.000;
- 0.000 -0.667 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- mkheaderreg = 0, float2int = 0
- ---- Input registration matrix --------
- 0.997 -0.031 -0.077 0.162;
- 0.079 0.080 0.994 -0.039;
- -0.025 -0.996 0.083 0.039;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub004
- RegMat ---------------------------
- 0.997 -0.031 -0.077 0.162;
- 0.079 0.080 0.994 -0.039;
- -0.025 -0.996 0.083 0.039;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.006 0.007 -0.048;
- 0.006 1.000 0.009 -0.013;
- -0.007 -0.009 1.000 0.261;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.698 -0.017 -0.053 45.936;
- -0.054 0.055 -0.662 251.945;
- 0.022 0.664 0.054 -12.768;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 21:37:12 CEST 2013
- Ended at Thu Aug 8 21:50:01 CEST 2013
- BBR-Run-Time-Sec 769
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/T2.mgz
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996814, 0.0369416, 0.0706971)
- j_ras = (0.0317143, 0.996777, -0.0736842)
- k_ras = (0.0731912, 0.0712073, 0.994773)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub004
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.006 0.007 -0.048;
- 0.006 1.000 0.009 -0.013;
- -0.007 -0.009 1.000 0.261;
- 0.000 0.000 0.000 1.000;
- ---------------------------------
- Applying LTAtransformInterp (resample_type 1)
- changing data type from float to uchar (noscale = 0)...
- MRIchangeType: Building histogram
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/T2.mgz
- using segmentation for initial intensity normalization
- using Gaussian smoothing of bias field, sigma=4.000
- reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 11592 non wm control points removed
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- smoothing bias field
- writing normalized volume to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub004 lh
- -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
- refining pial surfaces placement using T2 volume ../mri/T2
- using white starting white location...
- using woT2.pial starting pial locations...
- INFO: assuming MGZ format for volumes.
- using brain.finalsurfs as T1 volume...
- $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- 16986 bright wm thresholded.
- 439 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.orig...
- computing class statistics...
- border white: 249466 voxels (1.49%)
- border gray 280050 voxels (1.67%)
- WM (92.0): 93.6 +- 10.0 [70.0 --> 110.0]
- GM (76.0) : 73.8 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.1 (was 70)
- setting MAX_BORDER_WHITE to 115.0 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.1 (was 40)
- setting MAX_GRAY to 95.0 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.2 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 93.4, mean outside = 69.0
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.02-->4.18) (max @ vno 84931 --> 85959)
- face area 0.33 +- 0.15 (0.00-->3.00)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 107 points - only 7.48% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 5 with 21 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 589 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 11 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- deleting segment 14 with 7 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.03-->4.18) (max @ vno 85959 --> 84931)
- face area 0.33 +- 0.15 (0.00-->3.00)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4061406.2, rms=0.00
- rms = 1.35, time step reduction 1 of 3 to 0.250...
- rms = 0.34, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4061406.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 107 points - only 7.48% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 21 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 5 with 589 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.03-->4.18) (max @ vno 85959 --> 84931)
- face area 0.33 +- 0.15 (0.00-->3.00)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4061406.2, rms=0.00
- rms = 1.27, time step reduction 1 of 3 to 0.250...
- rms = 0.33, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4061406.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 107 points - only 7.48% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 21 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 5 with 589 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.03-->4.18) (max @ vno 85959 --> 84931)
- face area 0.33 +- 0.15 (0.00-->3.00)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4061406.2, rms=0.00
- rms = 1.35, time step reduction 1 of 3 to 0.250...
- rms = 0.34, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4061406.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 107 points - only 7.48% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 21 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 5 with 589 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4061406.2, rms=0.00
- rms = 1.27, time step reduction 1 of 3 to 0.250...
- rms = 0.33, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4061406.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [117.40 202.60], gm=160.00+-14.20, and vertices in regions > 152.9
- 42073 surface locations found to contain inconsistent values (12100 in, 29973 out)
- tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 1.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=488837.7, rms=0.37
- 001: dt: 0.5000, sse=458291.2, rms=0.360 (0.000%)
- 002: dt: 0.5000, sse=439636.8, rms=0.346 (0.000%)
- 003: dt: 0.5000, sse=428160.2, rms=0.334 (0.000%)
- 004: dt: 0.5000, sse=419136.5, rms=0.323 (0.000%)
- 005: dt: 0.5000, sse=412620.9, rms=0.313 (0.000%)
- 006: dt: 0.5000, sse=407977.7, rms=0.304 (0.000%)
- 007: dt: 0.5000, sse=404708.3, rms=0.295 (0.000%)
- 008: dt: 0.5000, sse=402426.3, rms=0.287 (0.000%)
- 009: dt: 0.5000, sse=400109.0, rms=0.279 (0.000%)
- 010: dt: 0.5000, sse=398470.2, rms=0.272 (0.000%)
- 011: dt: 0.5000, sse=397131.9, rms=0.265 (0.000%)
- 012: dt: 0.5000, sse=396065.1, rms=0.259 (0.000%)
- 013: dt: 0.5000, sse=395155.5, rms=0.253 (0.000%)
- 014: dt: 0.5000, sse=394772.1, rms=0.247 (0.000%)
- 015: dt: 0.5000, sse=393904.7, rms=0.241 (0.000%)
- 016: dt: 0.5000, sse=393300.7, rms=0.236 (0.000%)
- 017: dt: 0.5000, sse=392485.2, rms=0.231 (0.000%)
- 018: dt: 0.5000, sse=392192.4, rms=0.226 (0.000%)
- 019: dt: 0.5000, sse=391846.1, rms=0.222 (0.000%)
- 020: dt: 0.5000, sse=391388.2, rms=0.218 (0.000%)
- 021: dt: 0.5000, sse=390934.8, rms=0.214 (0.000%)
- 022: dt: 0.5000, sse=390278.8, rms=0.210 (0.000%)
- 023: dt: 0.5000, sse=389995.7, rms=0.206 (0.000%)
- 024: dt: 0.5000, sse=389432.5, rms=0.203 (0.000%)
- 025: dt: 0.5000, sse=388784.2, rms=0.200 (0.000%)
- 026: dt: 0.5000, sse=388671.6, rms=0.197 (0.000%)
- 027: dt: 0.5000, sse=388111.2, rms=0.195 (0.000%)
- 028: dt: 0.5000, sse=388136.2, rms=0.193 (0.000%)
- 029: dt: 0.5000, sse=387643.5, rms=0.191 (0.000%)
- 030: dt: 0.5000, sse=387312.3, rms=0.189 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [105.50 210.50], gm=158.00+-17.50, and vertices in regions > 149.2
- 29888 surface locations found to contain inconsistent values (1421 in, 28467 out)
- tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=40501.8, rms=0.14
- 031: dt: 0.5000, sse=40243.2, rms=0.135 (0.000%)
- 032: dt: 0.5000, sse=40877.7, rms=0.123 (0.000%)
- 033: dt: 0.5000, sse=41775.4, rms=0.115 (0.000%)
- 034: dt: 0.5000, sse=42582.8, rms=0.110 (0.000%)
- 035: dt: 0.5000, sse=43333.3, rms=0.105 (0.000%)
- 036: dt: 0.5000, sse=44062.6, rms=0.100 (0.000%)
- 037: dt: 0.5000, sse=44774.3, rms=0.095 (0.000%)
- 038: dt: 0.5000, sse=45480.4, rms=0.091 (0.000%)
- 039: dt: 0.5000, sse=46144.5, rms=0.087 (0.000%)
- 040: dt: 0.5000, sse=46815.3, rms=0.083 (0.000%)
- 041: dt: 0.5000, sse=47466.3, rms=0.080 (0.000%)
- 042: dt: 0.5000, sse=48062.2, rms=0.077 (0.000%)
- 043: dt: 0.5000, sse=48636.2, rms=0.074 (0.000%)
- 044: dt: 0.5000, sse=49177.6, rms=0.071 (0.000%)
- 045: dt: 0.5000, sse=49701.8, rms=0.069 (0.000%)
- 046: dt: 0.5000, sse=50162.6, rms=0.066 (0.000%)
- 047: dt: 0.5000, sse=50645.3, rms=0.064 (0.000%)
- 048: dt: 0.5000, sse=51113.2, rms=0.062 (0.000%)
- 049: dt: 0.5000, sse=51518.5, rms=0.060 (0.000%)
- 050: dt: 0.5000, sse=51937.0, rms=0.059 (0.000%)
- 051: dt: 0.5000, sse=52325.7, rms=0.057 (0.000%)
- 052: dt: 0.5000, sse=52704.5, rms=0.056 (0.000%)
- 053: dt: 0.5000, sse=53023.3, rms=0.054 (0.000%)
- 054: dt: 0.5000, sse=53320.8, rms=0.053 (0.000%)
- 055: dt: 0.5000, sse=53586.6, rms=0.052 (0.000%)
- 056: dt: 0.5000, sse=53849.2, rms=0.051 (0.000%)
- 057: dt: 0.5000, sse=54080.1, rms=0.050 (0.000%)
- 058: dt: 0.5000, sse=54323.8, rms=0.049 (0.000%)
- 059: dt: 0.5000, sse=54533.8, rms=0.048 (0.000%)
- 060: dt: 0.5000, sse=54706.9, rms=0.047 (0.000%)
- positioning took 3.7 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [97.00 223.00], gm=160.00+-21.00, and vertices in regions > 149.5
- 28987 surface locations found to contain inconsistent values (133 in, 28854 out)
- tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6755.0, rms=0.10
- 061: dt: 0.5000, sse=6583.4, rms=0.093 (0.000%)
- 062: dt: 0.5000, sse=6443.8, rms=0.081 (0.000%)
- 063: dt: 0.5000, sse=6412.1, rms=0.072 (0.000%)
- 064: dt: 0.5000, sse=6432.5, rms=0.066 (0.000%)
- 065: dt: 0.5000, sse=6477.2, rms=0.060 (0.000%)
- 066: dt: 0.5000, sse=6517.2, rms=0.056 (0.000%)
- 067: dt: 0.5000, sse=6548.2, rms=0.053 (0.000%)
- 068: dt: 0.5000, sse=6582.6, rms=0.050 (0.000%)
- 069: dt: 0.5000, sse=6624.9, rms=0.048 (0.000%)
- 070: dt: 0.5000, sse=6668.8, rms=0.045 (0.000%)
- 071: dt: 0.5000, sse=6715.2, rms=0.044 (0.000%)
- 072: dt: 0.5000, sse=6757.5, rms=0.042 (0.000%)
- 073: dt: 0.5000, sse=6800.4, rms=0.040 (0.000%)
- 074: dt: 0.5000, sse=6838.4, rms=0.039 (0.000%)
- 075: dt: 0.5000, sse=6870.2, rms=0.037 (0.000%)
- 076: dt: 0.5000, sse=6899.0, rms=0.036 (0.000%)
- 077: dt: 0.5000, sse=6923.1, rms=0.035 (0.000%)
- 078: dt: 0.5000, sse=6944.8, rms=0.034 (0.000%)
- 079: dt: 0.5000, sse=6963.5, rms=0.033 (0.000%)
- 080: dt: 0.5000, sse=6985.0, rms=0.032 (0.000%)
- 081: dt: 0.5000, sse=7002.3, rms=0.032 (0.000%)
- 082: dt: 0.5000, sse=7021.0, rms=0.031 (0.000%)
- 083: dt: 0.5000, sse=7038.0, rms=0.031 (0.000%)
- 084: dt: 0.5000, sse=7051.4, rms=0.031 (0.000%)
- 085: dt: 0.5000, sse=7065.4, rms=0.030 (0.000%)
- 086: dt: 0.5000, sse=7076.5, rms=0.030 (0.000%)
- 087: dt: 0.5000, sse=7087.7, rms=0.030 (0.000%)
- 088: dt: 0.5000, sse=7094.5, rms=0.029 (0.000%)
- 089: dt: 0.5000, sse=7101.0, rms=0.029 (0.000%)
- 090: dt: 0.5000, sse=7105.9, rms=0.029 (0.000%)
- positioning took 3.7 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [84.80 231.20], gm=158.00+-24.40, and vertices in regions > 145.8
- 28101 surface locations found to contain inconsistent values (21 in, 28080 out)
- tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000
- mom=0.00, dt=0.50
- writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1189.6, rms=0.06
- 091: dt: 0.5000, sse=1100.0, rms=0.055 (0.000%)
- 092: dt: 0.5000, sse=997.6, rms=0.046 (0.000%)
- 093: dt: 0.5000, sse=957.1, rms=0.042 (0.000%)
- 094: dt: 0.5000, sse=937.3, rms=0.039 (0.000%)
- 095: dt: 0.5000, sse=921.2, rms=0.036 (0.000%)
- 096: dt: 0.5000, sse=912.1, rms=0.035 (0.000%)
- 097: dt: 0.5000, sse=904.3, rms=0.033 (0.000%)
- 098: dt: 0.5000, sse=899.2, rms=0.032 (0.000%)
- 099: dt: 0.5000, sse=895.0, rms=0.032 (0.000%)
- 100: dt: 0.5000, sse=892.1, rms=0.031 (0.000%)
- 101: dt: 0.5000, sse=889.6, rms=0.030 (0.000%)
- 102: dt: 0.5000, sse=887.2, rms=0.030 (0.000%)
- 103: dt: 0.5000, sse=884.9, rms=0.029 (0.000%)
- 104: dt: 0.5000, sse=884.3, rms=0.029 (0.000%)
- 105: dt: 0.5000, sse=883.2, rms=0.029 (0.000%)
- 106: dt: 0.5000, sse=881.8, rms=0.028 (0.000%)
- 107: dt: 0.5000, sse=881.4, rms=0.028 (0.000%)
- 108: dt: 0.5000, sse=881.3, rms=0.028 (0.000%)
- 109: dt: 0.5000, sse=879.9, rms=0.028 (0.000%)
- 110: dt: 0.5000, sse=878.8, rms=0.028 (0.000%)
- 111: dt: 0.5000, sse=878.4, rms=0.028 (0.000%)
- 112: dt: 0.5000, sse=877.8, rms=0.028 (0.000%)
- 113: dt: 0.5000, sse=877.5, rms=0.027 (0.000%)
- 114: dt: 0.5000, sse=877.1, rms=0.027 (0.000%)
- 115: dt: 0.5000, sse=877.5, rms=0.027 (0.000%)
- 116: dt: 0.5000, sse=879.2, rms=0.028 (0.000%)
- 117: dt: 0.5000, sse=878.5, rms=0.027 (0.000%)
- 118: dt: 0.5000, sse=877.7, rms=0.027 (0.000%)
- 119: dt: 0.5000, sse=876.3, rms=0.027 (0.000%)
- 120: dt: 0.5000, sse=875.9, rms=0.027 (0.000%)
- positioning took 3.9 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.area.pial
- vertex spacing 1.02 +- 0.44 (0.05-->7.20) (max @ vno 97893 --> 98996)
- face area 0.41 +- 0.31 (0.00-->5.13)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 135159 vertices processed
- 25000 of 135159 vertices processed
- 50000 of 135159 vertices processed
- 75000 of 135159 vertices processed
- 100000 of 135159 vertices processed
- 125000 of 135159 vertices processed
- 0 of 135159 vertices processed
- 25000 of 135159 vertices processed
- 50000 of 135159 vertices processed
- 75000 of 135159 vertices processed
- 100000 of 135159 vertices processed
- 125000 of 135159 vertices processed
- thickness calculation complete, 283:572 truncations.
- 32033 vertices at 0 distance
- 93093 vertices at 1 distance
- 84187 vertices at 2 distance
- 34398 vertices at 3 distance
- 10363 vertices at 4 distance
- 2990 vertices at 5 distance
- 832 vertices at 6 distance
- 287 vertices at 7 distance
- 92 vertices at 8 distance
- 42 vertices at 9 distance
- 52 vertices at 10 distance
- 38 vertices at 11 distance
- 31 vertices at 12 distance
- 17 vertices at 13 distance
- 15 vertices at 14 distance
- 15 vertices at 15 distance
- 10 vertices at 16 distance
- 4 vertices at 17 distance
- 7 vertices at 18 distance
- 9 vertices at 19 distance
- 5 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.thickness
- positioning took 19.3 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub004 rh
- -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
- refining pial surfaces placement using T2 volume ../mri/T2
- using white starting white location...
- using woT2.pial starting pial locations...
- INFO: assuming MGZ format for volumes.
- using brain.finalsurfs as T1 volume...
- $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- 16676 bright wm thresholded.
- 447 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.orig...
- computing class statistics...
- border white: 249466 voxels (1.49%)
- border gray 280050 voxels (1.67%)
- WM (92.0): 93.5 +- 9.9 [70.0 --> 110.0]
- GM (76.0) : 73.7 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 45.7 (was 70)
- setting MAX_BORDER_WHITE to 114.9 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 32.5 (was 40)
- setting MAX_GRAY to 95.1 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 19.2 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 93.1, mean outside = 68.7
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.04-->7.55) (max @ vno 57288 --> 57289)
- face area 0.33 +- 0.16 (0.00-->6.93)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 4 with 16 points - only 0.00% unknown
- deleting segment 5 with 19 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 359 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- deleting segment 9 with 19 points - only 0.00% unknown
- deleting segment 11 with 27 points - only 0.00% unknown
- deleting segment 12 with 69 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 13 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 14 with 1 points - only 0.00% unknown
- deleting segment 15 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.09-->7.55) (max @ vno 57289 --> 57288)
- face area 0.33 +- 0.16 (0.00-->6.93)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4265086.0, rms=0.00
- rms = 1.44, time step reduction 1 of 3 to 0.250...
- rms = 0.37, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4265086.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- deleting segment 3 with 16 points - only 0.00% unknown
- deleting segment 4 with 19 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 359 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- deleting segment 8 with 19 points - only 0.00% unknown
- deleting segment 9 with 27 points - only 0.00% unknown
- deleting segment 10 with 69 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- deleting segment 13 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.09-->7.55) (max @ vno 57289 --> 57288)
- face area 0.33 +- 0.16 (0.00-->6.93)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4265086.0, rms=0.00
- rms = 1.44, time step reduction 1 of 3 to 0.250...
- rms = 0.37, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4265086.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- deleting segment 3 with 16 points - only 0.00% unknown
- deleting segment 4 with 19 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 359 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- deleting segment 8 with 19 points - only 0.00% unknown
- deleting segment 9 with 27 points - only 0.00% unknown
- deleting segment 10 with 69 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- deleting segment 13 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.09-->7.55) (max @ vno 57289 --> 57288)
- face area 0.33 +- 0.16 (0.00-->6.93)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4265086.0, rms=0.00
- rms = 1.44, time step reduction 1 of 3 to 0.250...
- rms = 0.37, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4265086.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- deleting segment 3 with 16 points - only 0.00% unknown
- deleting segment 4 with 19 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 359 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- deleting segment 8 with 19 points - only 0.00% unknown
- deleting segment 9 with 27 points - only 0.00% unknown
- deleting segment 10 with 69 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- deleting segment 13 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4265086.0, rms=0.00
- rms = 1.44, time step reduction 1 of 3 to 0.250...
- rms = 0.37, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4265086.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [99.80 222.20], gm=161.00+-20.40, and vertices in regions > 150.8
- 31008 surface locations found to contain inconsistent values (4401 in, 26607 out)
- tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 1.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=490804.9, rms=0.24
- 001: dt: 0.5000, sse=458243.6, rms=0.234 (0.000%)
- 002: dt: 0.5000, sse=438987.0, rms=0.221 (0.000%)
- 003: dt: 0.5000, sse=427149.1, rms=0.211 (0.000%)
- 004: dt: 0.5000, sse=418223.1, rms=0.202 (0.000%)
- 005: dt: 0.5000, sse=411889.3, rms=0.194 (0.000%)
- 006: dt: 0.5000, sse=407517.5, rms=0.187 (0.000%)
- 007: dt: 0.5000, sse=404621.2, rms=0.181 (0.000%)
- 008: dt: 0.5000, sse=401832.6, rms=0.176 (0.000%)
- 009: dt: 0.5000, sse=399988.4, rms=0.172 (0.000%)
- 010: dt: 0.5000, sse=398540.8, rms=0.168 (0.000%)
- 011: dt: 0.5000, sse=397376.3, rms=0.164 (0.000%)
- 012: dt: 0.5000, sse=395608.5, rms=0.161 (0.000%)
- 013: dt: 0.5000, sse=395169.8, rms=0.159 (0.000%)
- 014: dt: 0.5000, sse=393793.7, rms=0.156 (0.000%)
- 015: dt: 0.5000, sse=393000.9, rms=0.155 (0.000%)
- 016: dt: 0.5000, sse=390916.3, rms=0.153 (0.000%)
- 017: dt: 0.5000, sse=390420.2, rms=0.152 (0.000%)
- 018: dt: 0.5000, sse=389245.7, rms=0.150 (0.000%)
- 019: dt: 0.5000, sse=388067.8, rms=0.150 (0.000%)
- 020: dt: 0.5000, sse=386642.1, rms=0.149 (0.000%)
- 021: dt: 0.5000, sse=386081.9, rms=0.148 (0.000%)
- 022: dt: 0.5000, sse=384651.1, rms=0.148 (0.000%)
- 023: dt: 0.5000, sse=383901.5, rms=0.147 (0.000%)
- 024: dt: 0.5000, sse=382736.2, rms=0.147 (0.000%)
- 025: dt: 0.5000, sse=381569.7, rms=0.147 (0.000%)
- 026: dt: 0.5000, sse=380438.9, rms=0.147 (0.000%)
- 027: dt: 0.5000, sse=379862.5, rms=0.147 (0.000%)
- 028: dt: 0.5000, sse=378875.7, rms=0.147 (0.000%)
- 029: dt: 0.5000, sse=378313.2, rms=0.147 (0.000%)
- 030: dt: 0.5000, sse=377410.2, rms=0.147 (0.000%)
- positioning took 3.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [99.50 222.50], gm=161.00+-20.50, and vertices in regions > 150.7
- 24390 surface locations found to contain inconsistent values (1589 in, 22801 out)
- tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=39353.0, rms=0.13
- 031: dt: 0.5000, sse=39136.3, rms=0.123 (0.000%)
- 032: dt: 0.5000, sse=40033.5, rms=0.113 (0.000%)
- 033: dt: 0.5000, sse=41028.7, rms=0.105 (0.000%)
- 034: dt: 0.5000, sse=41981.5, rms=0.100 (0.000%)
- 035: dt: 0.5000, sse=42732.7, rms=0.095 (0.000%)
- 036: dt: 0.5000, sse=43489.2, rms=0.090 (0.000%)
- 037: dt: 0.5000, sse=44118.9, rms=0.086 (0.000%)
- 038: dt: 0.5000, sse=44871.6, rms=0.081 (0.000%)
- 039: dt: 0.5000, sse=45498.0, rms=0.078 (0.000%)
- 040: dt: 0.5000, sse=46191.1, rms=0.074 (0.000%)
- 041: dt: 0.5000, sse=46790.5, rms=0.071 (0.000%)
- 042: dt: 0.5000, sse=47453.0, rms=0.068 (0.000%)
- 043: dt: 0.5000, sse=47961.4, rms=0.065 (0.000%)
- 044: dt: 0.5000, sse=48542.1, rms=0.063 (0.000%)
- 045: dt: 0.5000, sse=48972.1, rms=0.061 (0.000%)
- 046: dt: 0.5000, sse=49471.3, rms=0.059 (0.000%)
- 047: dt: 0.5000, sse=49861.1, rms=0.056 (0.000%)
- 048: dt: 0.5000, sse=50271.8, rms=0.055 (0.000%)
- 049: dt: 0.5000, sse=50624.3, rms=0.053 (0.000%)
- 050: dt: 0.5000, sse=50986.8, rms=0.051 (0.000%)
- 051: dt: 0.5000, sse=51290.1, rms=0.050 (0.000%)
- 052: dt: 0.5000, sse=51643.7, rms=0.049 (0.000%)
- 053: dt: 0.5000, sse=51884.0, rms=0.047 (0.000%)
- 054: dt: 0.5000, sse=52159.9, rms=0.046 (0.000%)
- 055: dt: 0.5000, sse=52354.6, rms=0.045 (0.000%)
- 056: dt: 0.5000, sse=52619.2, rms=0.044 (0.000%)
- 057: dt: 0.5000, sse=52806.8, rms=0.043 (0.000%)
- 058: dt: 0.5000, sse=53010.9, rms=0.042 (0.000%)
- 059: dt: 0.5000, sse=53182.8, rms=0.041 (0.000%)
- 060: dt: 0.5000, sse=53341.6, rms=0.041 (0.000%)
- positioning took 4.6 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [99.00 225.00], gm=162.00+-21.00, and vertices in regions > 151.5
- 23530 surface locations found to contain inconsistent values (275 in, 23255 out)
- tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5690.9, rms=0.05
- 061: dt: 0.5000, sse=5675.2, rms=0.051 (0.000%)
- 062: dt: 0.5000, sse=5784.3, rms=0.044 (0.000%)
- 063: dt: 0.5000, sse=5881.8, rms=0.041 (0.000%)
- 064: dt: 0.5000, sse=5959.8, rms=0.039 (0.000%)
- 065: dt: 0.5000, sse=6006.5, rms=0.036 (0.000%)
- 066: dt: 0.5000, sse=6035.0, rms=0.035 (0.000%)
- 067: dt: 0.5000, sse=6053.1, rms=0.034 (0.000%)
- 068: dt: 0.5000, sse=6067.9, rms=0.033 (0.000%)
- 069: dt: 0.5000, sse=6080.3, rms=0.032 (0.000%)
- 070: dt: 0.5000, sse=6093.9, rms=0.031 (0.000%)
- 071: dt: 0.5000, sse=6106.5, rms=0.030 (0.000%)
- 072: dt: 0.5000, sse=6117.8, rms=0.029 (0.000%)
- 073: dt: 0.5000, sse=6127.4, rms=0.029 (0.000%)
- 074: dt: 0.5000, sse=6136.5, rms=0.028 (0.000%)
- 075: dt: 0.5000, sse=6144.9, rms=0.028 (0.000%)
- 076: dt: 0.5000, sse=6149.0, rms=0.027 (0.000%)
- 077: dt: 0.5000, sse=6152.1, rms=0.027 (0.000%)
- 078: dt: 0.5000, sse=6155.4, rms=0.026 (0.000%)
- 079: dt: 0.5000, sse=6156.6, rms=0.026 (0.000%)
- 080: dt: 0.5000, sse=6163.8, rms=0.026 (0.000%)
- 081: dt: 0.5000, sse=6164.9, rms=0.026 (0.000%)
- 082: dt: 0.5000, sse=6166.1, rms=0.025 (0.000%)
- 083: dt: 0.5000, sse=6170.3, rms=0.025 (0.000%)
- 084: dt: 0.5000, sse=6173.1, rms=0.025 (0.000%)
- 085: dt: 0.5000, sse=6175.6, rms=0.025 (0.000%)
- 086: dt: 0.5000, sse=6181.2, rms=0.025 (0.000%)
- 087: dt: 0.5000, sse=6180.3, rms=0.025 (0.000%)
- 088: dt: 0.5000, sse=6183.3, rms=0.025 (0.000%)
- 089: dt: 0.5000, sse=6185.7, rms=0.025 (0.000%)
- 090: dt: 0.5000, sse=6185.4, rms=0.024 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [97.80 226.20], gm=162.00+-21.40, and vertices in regions > 151.3
- 23323 surface locations found to contain inconsistent values (61 in, 23262 out)
- tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000
- mom=0.00, dt=0.50
- writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=742.3, rms=0.03
- 091: dt: 0.5000, sse=739.0, rms=0.031 (0.000%)
- 092: dt: 0.5000, sse=719.1, rms=0.028 (0.000%)
- 093: dt: 0.5000, sse=713.3, rms=0.026 (0.000%)
- 094: dt: 0.5000, sse=710.3, rms=0.025 (0.000%)
- 095: dt: 0.5000, sse=707.9, rms=0.025 (0.000%)
- 096: dt: 0.5000, sse=706.4, rms=0.024 (0.000%)
- 097: dt: 0.5000, sse=706.0, rms=0.024 (0.000%)
- 098: dt: 0.5000, sse=704.9, rms=0.024 (0.000%)
- 099: dt: 0.5000, sse=703.3, rms=0.024 (0.000%)
- 100: dt: 0.5000, sse=702.0, rms=0.023 (0.000%)
- 101: dt: 0.5000, sse=701.0, rms=0.023 (0.000%)
- 102: dt: 0.5000, sse=700.3, rms=0.023 (0.000%)
- 103: dt: 0.5000, sse=699.4, rms=0.023 (0.000%)
- 104: dt: 0.5000, sse=698.4, rms=0.023 (0.000%)
- 105: dt: 0.5000, sse=698.3, rms=0.023 (0.000%)
- 106: dt: 0.5000, sse=697.2, rms=0.022 (0.000%)
- 107: dt: 0.5000, sse=696.6, rms=0.022 (0.000%)
- 108: dt: 0.5000, sse=695.7, rms=0.022 (0.000%)
- 109: dt: 0.5000, sse=695.6, rms=0.022 (0.000%)
- 110: dt: 0.5000, sse=694.9, rms=0.022 (0.000%)
- 111: dt: 0.5000, sse=694.5, rms=0.022 (0.000%)
- 112: dt: 0.5000, sse=693.5, rms=0.022 (0.000%)
- 113: dt: 0.5000, sse=693.4, rms=0.022 (0.000%)
- 114: dt: 0.5000, sse=693.2, rms=0.022 (0.000%)
- 115: dt: 0.5000, sse=692.8, rms=0.022 (0.000%)
- 116: dt: 0.5000, sse=692.6, rms=0.022 (0.000%)
- 117: dt: 0.5000, sse=693.1, rms=0.022 (0.000%)
- 118: dt: 0.5000, sse=692.9, rms=0.022 (0.000%)
- 119: dt: 0.5000, sse=692.7, rms=0.021 (0.000%)
- 120: dt: 0.5000, sse=692.5, rms=0.021 (0.000%)
- positioning took 3.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.area.pial
- vertex spacing 1.02 +- 0.44 (0.07-->8.36) (max @ vno 57289 --> 57288)
- face area 0.41 +- 0.31 (0.00-->6.40)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 134900 vertices processed
- 25000 of 134900 vertices processed
- 50000 of 134900 vertices processed
- 75000 of 134900 vertices processed
- 100000 of 134900 vertices processed
- 125000 of 134900 vertices processed
- 0 of 134900 vertices processed
- 25000 of 134900 vertices processed
- 50000 of 134900 vertices processed
- 75000 of 134900 vertices processed
- 100000 of 134900 vertices processed
- 125000 of 134900 vertices processed
- thickness calculation complete, 490:493 truncations.
- 27694 vertices at 0 distance
- 88109 vertices at 1 distance
- 87374 vertices at 2 distance
- 38363 vertices at 3 distance
- 12049 vertices at 4 distance
- 3571 vertices at 5 distance
- 1005 vertices at 6 distance
- 310 vertices at 7 distance
- 105 vertices at 8 distance
- 50 vertices at 9 distance
- 36 vertices at 10 distance
- 35 vertices at 11 distance
- 23 vertices at 12 distance
- 23 vertices at 13 distance
- 27 vertices at 14 distance
- 11 vertices at 15 distance
- 9 vertices at 16 distance
- 10 vertices at 17 distance
- 5 vertices at 18 distance
- 6 vertices at 19 distance
- 23 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.thickness
- positioning took 20.7 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 22:31:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 22:31:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Cortical ribbon mask Thu Aug 8 22:31:46 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub004
- SUBJECTS_DIR is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- loading input data...
- computing distance to left white surface
- computing distance to left pial surface
- computing distance to right white surface
- computing distance to right pial surface
- hemi masks overlap voxels = 24
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Thu Aug 8 22:49:52 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004
- mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/5.3.0/ASegStatsLUT.txt --subject sub004
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/5.3.0/ASegStatsLUT.txt --subject sub004
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1146800 mm^3 (det: 1.698731 )
- Computing euler number
- orig.nofix lheno = -24, rheno = -32
- orig.nofix lhholes = 13, rhholes = 17
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 245603.857 244375.000 diff= 1228.9 pctdiff= 0.500
- rhCtxGM: 247416.963 246534.000 diff= 883.0 pctdiff= 0.357
- lhCtxWM: 216143.446 216369.000 diff= -225.6 pctdiff=-0.104
- rhCtxWM: 224219.700 223929.000 diff= 290.7 pctdiff= 0.130
- SubCortGMVol 69284.000
- SupraTentVol 1013770.966 (1010736.000) diff=3034.966 pctdiff=0.299
- SupraTentVolNotVent 1003808.966 (1000774.000) diff=3034.966 pctdiff=0.302
- BrainSegVol 1151940.000 (1149275.000) diff=2665.000 pctdiff=0.231
- BrainSegVolNotVent 1138507.000 (1140454.966) diff=-1947.966 pctdiff=-0.171
- BrainSegVolNotVent 1138507.000
- CerebellumVol 137504.000
- VentChorVol 9962.000
- 3rd4th5thCSF 3471.000
- CSFVol 824.000, OptChiasmVol 211.000
- MaskVol 1596634.000
- Loading mri/norm.mgz
- Loading mri/norm.mgz
- Voxel Volume is 1 mm^3
- Generating list of segmentation ids
- Found 50 segmentations
- Computing statistics for each segmentation
- 3 4 Left-Lateral-Ventricle 3581 3580.592
- 4 5 Left-Inf-Lat-Vent 556 555.928
- 5 7 Left-Cerebellum-White-Matter 14525 14525.024
- 6 8 Left-Cerebellum-Cortex 54206 54205.590
- 7 10 Left-Thalamus-Proper 9072 9071.589
- 8 11 Left-Caudate 4223 4222.505
- 9 12 Left-Putamen 6940 6940.056
- 10 13 Left-Pallidum 2242 2241.858
- 11 14 3rd-Ventricle 519 519.106
- 12 15 4th-Ventricle 2351 2350.718
- 13 16 Brain-Stem 21530 21529.875
- 14 17 Left-Hippocampus 4111 4111.180
- 15 18 Left-Amygdala 1762 1761.773
- 16 24 CSF 818 818.213
- 17 26 Left-Accumbens-area 777 776.739
- 18 28 Left-VentralDC 4598 4598.338
- 19 30 Left-vessel 93 92.757
- 20 31 Left-choroid-plexus 959 959.462
- 23 43 Right-Lateral-Ventricle 3415 3414.959
- 24 44 Right-Inf-Lat-Vent 333 333.328
- 25 46 Right-Cerebellum-White-Matter 15065 15064.798
- 26 47 Right-Cerebellum-Cortex 56389 56389.203
- 27 49 Right-Thalamus-Proper 7571 7570.675
- 28 50 Right-Caudate 4221 4221.152
- 29 51 Right-Putamen 6773 6773.270
- 30 52 Right-Pallidum 2764 2763.700
- 31 53 Right-Hippocampus 4527 4526.754
- 32 54 Right-Amygdala 2054 2054.351
- 33 58 Right-Accumbens-area 828 827.652
- 34 60 Right-VentralDC 4491 4490.870
- 35 62 Right-vessel 164 164.479
- 36 63 Right-choroid-plexus 1229 1228.974
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 944 944.009
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 20 20.217
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 211 210.521
- 45 251 CC_Posterior 694 694.332
- 46 252 CC_Mid_Posterior 315 314.981
- 47 253 CC_Central 378 378.170
- 48 254 CC_Mid_Anterior 455 454.644
- 49 255 CC_Anterior 838 837.945
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Thu Aug 8 22:54:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004
- mri_aparc2aseg --s sub004 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub004
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.aparc.annot
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Reading rh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.aparc.annot
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Have color table for lh white annotation
- Have color table for rh white annotation
- Loading ribbon segmentation from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/ribbon.mgz
- Building hash of lh white
- Building hash of lh pial
- Building hash of rh white
- Building hash of rh pial
- Loading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz
- ASeg Vox2RAS: -----------
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- -------------------------
- Labeling Slice
- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
- 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
- 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
- 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
- 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
- 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
- 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
- 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
- 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
- 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
- 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 489248
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004
- mri_aparc2aseg --s sub004 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub004
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.aparc.a2009s.annot
- reading colortable from annotation file...
- colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
- Reading rh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.aparc.a2009s.annot
- reading colortable from annotation file...
- colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
- Have color table for lh white annotation
- Have color table for rh white annotation
- Loading ribbon segmentation from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/ribbon.mgz
- Building hash of lh white
- Building hash of lh pial
- Building hash of rh white
- Building hash of rh pial
- Loading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz
- ASeg Vox2RAS: -----------
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- -------------------------
- Labeling Slice
- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
- 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
- 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
- 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
- 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
- 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
- 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
- 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
- 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
- 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
- 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 489248
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Thu Aug 8 23:00:04 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004
- mri_aparc2aseg --s sub004 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub004
- outvol mri/wmparc.mgz
- useribbon 0
- baseoffset 0
- labeling wm
- labeling hypo-intensities as wm
- dmaxctx 5.000000
- RipUnknown 1
- CtxSeg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.aparc.annot
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Reading rh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.aparc.annot
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Have color table for lh white annotation
- Have color table for rh white annotation
- Loading ribbon segmentation from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 8149 vertices from left hemi
- Ripped 7339 vertices from right hemi
- Building hash of lh white
- Building hash of lh pial
- Building hash of rh white
- Building hash of rh pial
- Loading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/aparc+aseg.mgz
- ASeg Vox2RAS: -----------
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- -------------------------
- Labeling Slice
- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
- 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
- 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
- 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
- 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
- 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
- 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
- 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
- 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
- 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
- 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 928378
- Used brute-force search on 116 voxels
- Fixing Parahip LH WM
- Found 16 clusters
- 0 k 1.000000
- 1 k 1.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 5.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 3.000000
- 8 k 1.000000
- 9 k 1.000000
- 10 k 11.000000
- 11 k 2.000000
- 12 k 1420.000000
- 13 k 1.000000
- 14 k 1.000000
- 15 k 1.000000
- Fixing Parahip RH WM
- Found 9 clusters
- 0 k 1.000000
- 1 k 5.000000
- 2 k 1375.000000
- 3 k 1.000000
- 4 k 9.000000
- 5 k 6.000000
- 6 k 1.000000
- 7 k 1.000000
- 8 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004
- mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub004 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub004 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1146800 mm^3 (det: 1.698731 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 245603.857 244375.000 diff= 1228.9 pctdiff= 0.500
- rhCtxGM: 247416.963 246534.000 diff= 883.0 pctdiff= 0.357
- lhCtxWM: 216143.446 216369.000 diff= -225.6 pctdiff=-0.104
- rhCtxWM: 224219.700 223929.000 diff= 290.7 pctdiff= 0.130
- SubCortGMVol 69284.000
- SupraTentVol 1013770.966 (1010736.000) diff=3034.966 pctdiff=0.299
- SupraTentVolNotVent 1003808.966 (1000774.000) diff=3034.966 pctdiff=0.302
- BrainSegVol 1151940.000 (1149275.000) diff=2665.000 pctdiff=0.231
- BrainSegVolNotVent 1138507.000 (1140454.966) diff=-1947.966 pctdiff=-0.171
- BrainSegVolNotVent 1138507.000
- CerebellumVol 137504.000
- VentChorVol 9962.000
- 3rd4th5thCSF 3471.000
- CSFVol 824.000, OptChiasmVol 211.000
- MaskVol 1596634.000
- Loading mri/norm.mgz
- Loading mri/norm.mgz
- Voxel Volume is 1 mm^3
- Generating list of segmentation ids
- Found 390 segmentations
- Computing statistics for each segmentation
- 0 3000 wm-lh-unknown 0 0.000
- 1 3001 wm-lh-bankssts 3430 3429.535
- 2 3002 wm-lh-caudalanteriorcingulate 3072 3071.681
- 3 3003 wm-lh-caudalmiddlefrontal 6882 6882.192
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2474 2474.209
- 6 3006 wm-lh-entorhinal 1131 1131.141
- 7 3007 wm-lh-fusiform 7046 7046.485
- 8 3008 wm-lh-inferiorparietal 9947 9946.780
- 9 3009 wm-lh-inferiortemporal 6573 6572.687
- 10 3010 wm-lh-isthmuscingulate 2922 2921.517
- 11 3011 wm-lh-lateraloccipital 9817 9816.721
- 12 3012 wm-lh-lateralorbitofrontal 6654 6654.363
- 13 3013 wm-lh-lingual 4892 4892.021
- 14 3014 wm-lh-medialorbitofrontal 2614 2613.994
- 15 3015 wm-lh-middletemporal 6059 6058.621
- 16 3016 wm-lh-parahippocampal 1480 1479.828
- 17 3017 wm-lh-paracentral 3244 3243.627
- 18 3018 wm-lh-parsopercularis 3601 3601.292
- 19 3019 wm-lh-parsorbitalis 876 876.372
- 20 3020 wm-lh-parstriangularis 2589 2588.561
- 21 3021 wm-lh-pericalcarine 3509 3508.599
- 22 3022 wm-lh-postcentral 7005 7004.896
- 23 3023 wm-lh-posteriorcingulate 4383 4382.862
- 24 3024 wm-lh-precentral 11179 11178.685
- 25 3025 wm-lh-precuneus 8174 8173.935
- 26 3026 wm-lh-rostralanteriorcingulate 2578 2578.419
- 27 3027 wm-lh-rostralmiddlefrontal 11866 11865.657
- 28 3028 wm-lh-superiorfrontal 18215 18214.930
- 29 3029 wm-lh-superiorparietal 11089 11088.910
- 30 3030 wm-lh-superiortemporal 7672 7671.691
- 31 3031 wm-lh-supramarginal 7906 7905.925
- 32 3032 wm-lh-frontalpole 172 172.000
- 33 3033 wm-lh-temporalpole 732 731.808
- 34 3034 wm-lh-transversetemporal 741 741.038
- 35 3035 wm-lh-insula 7878 7878.291
- 36 3100 wm-lh-Unknown 0 0.000
- 37 3101 wm-lh-Corpus_callosum 0 0.000
- 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000
- 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000
- 40 3104 wm-lh-G_cingulate-Main_part 0 0.000
- 41 3105 wm-lh-G_cuneus 0 0.000
- 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000
- 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000
- 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000
- 45 3109 wm-lh-G_frontal_middle 0 0.000
- 46 3110 wm-lh-G_frontal_superior 0 0.000
- 47 3111 wm-lh-G_frontomarginal 0 0.000
- 48 3112 wm-lh-G_insular_long 0 0.000
- 49 3113 wm-lh-G_insular_short 0 0.000
- 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000
- 51 3115 wm-lh-G_occipital_middle 0 0.000
- 52 3116 wm-lh-G_occipital_superior 0 0.000
- 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000
- 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000
- 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000
- 56 3120 wm-lh-G_orbital 0 0.000
- 57 3121 wm-lh-G_paracentral 0 0.000
- 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000
- 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000
- 60 3124 wm-lh-G_parietal_superior 0 0.000
- 61 3125 wm-lh-G_postcentral 0 0.000
- 62 3126 wm-lh-G_precentral 0 0.000
- 63 3127 wm-lh-G_precuneus 0 0.000
- 64 3128 wm-lh-G_rectus 0 0.000
- 65 3129 wm-lh-G_subcallosal 0 0.000
- 66 3130 wm-lh-G_subcentral 0 0.000
- 67 3131 wm-lh-G_temporal_inferior 0 0.000
- 68 3132 wm-lh-G_temporal_middle 0 0.000
- 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000
- 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000
- 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000
- 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000
- 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000
- 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000
- 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000
- 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000
- 77 3141 wm-lh-Medial_wall 0 0.000
- 78 3142 wm-lh-Pole_occipital 0 0.000
- 79 3143 wm-lh-Pole_temporal 0 0.000
- 80 3144 wm-lh-S_calcarine 0 0.000
- 81 3145 wm-lh-S_central 0 0.000
- 82 3146 wm-lh-S_central_insula 0 0.000
- 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000
- 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000
- 85 3149 wm-lh-S_circular_insula_anterior 0 0.000
- 86 3150 wm-lh-S_circular_insula_inferior 0 0.000
- 87 3151 wm-lh-S_circular_insula_superior 0 0.000
- 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000
- 89 3153 wm-lh-S_collateral_transverse_post 0 0.000
- 90 3154 wm-lh-S_frontal_inferior 0 0.000
- 91 3155 wm-lh-S_frontal_middle 0 0.000
- 92 3156 wm-lh-S_frontal_superior 0 0.000
- 93 3157 wm-lh-S_frontomarginal 0 0.000
- 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000
- 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000
- 96 3160 wm-lh-S_occipital_anterior 0 0.000
- 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000
- 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000
- 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000
- 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000
- 101 3165 wm-lh-S_orbital-H_shapped 0 0.000
- 102 3166 wm-lh-S_orbital_lateral 0 0.000
- 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000
- 104 3168 wm-lh-S_paracentral 0 0.000
- 105 3169 wm-lh-S_parieto_occipital 0 0.000
- 106 3170 wm-lh-S_pericallosal 0 0.000
- 107 3171 wm-lh-S_postcentral 0 0.000
- 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000
- 109 3173 wm-lh-S_precentral-Superior-part 0 0.000
- 110 3174 wm-lh-S_subcentral_ant 0 0.000
- 111 3175 wm-lh-S_subcentral_post 0 0.000
- 112 3176 wm-lh-S_suborbital 0 0.000
- 113 3177 wm-lh-S_subparietal 0 0.000
- 114 3178 wm-lh-S_supracingulate 0 0.000
- 115 3179 wm-lh-S_temporal_inferior 0 0.000
- 116 3180 wm-lh-S_temporal_superior 0 0.000
- 117 3181 wm-lh-S_temporal_transverse 0 0.000
- 118 4000 wm-rh-unknown 0 0.000
- 119 4001 wm-rh-bankssts 3165 3164.861
- 120 4002 wm-rh-caudalanteriorcingulate 3040 3039.821
- 121 4003 wm-rh-caudalmiddlefrontal 5661 5660.582
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 1997 1996.574
- 124 4006 wm-rh-entorhinal 726 725.562
- 125 4007 wm-rh-fusiform 6099 6098.587
- 126 4008 wm-rh-inferiorparietal 13752 13751.517
- 127 4009 wm-rh-inferiortemporal 6162 6161.637
- 128 4010 wm-rh-isthmuscingulate 2838 2837.558
- 129 4011 wm-rh-lateraloccipital 8924 8923.777
- 130 4012 wm-rh-lateralorbitofrontal 6898 6898.305
- 131 4013 wm-rh-lingual 5965 5965.293
- 132 4014 wm-rh-medialorbitofrontal 3687 3686.657
- 133 4015 wm-rh-middletemporal 6771 6770.654
- 134 4016 wm-rh-parahippocampal 1422 1422.330
- 135 4017 wm-rh-paracentral 4300 4300.492
- 136 4018 wm-rh-parsopercularis 3819 3819.382
- 137 4019 wm-rh-parsorbitalis 1366 1366.390
- 138 4020 wm-rh-parstriangularis 3744 3744.087
- 139 4021 wm-rh-pericalcarine 3221 3221.334
- 140 4022 wm-rh-postcentral 6547 6546.666
- 141 4023 wm-rh-posteriorcingulate 4196 4195.557
- 142 4024 wm-rh-precentral 11868 11867.850
- 143 4025 wm-rh-precuneus 8734 8733.638
- 144 4026 wm-rh-rostralanteriorcingulate 2297 2296.870
- 145 4027 wm-rh-rostralmiddlefrontal 13913 13913.246
- 146 4028 wm-rh-superiorfrontal 16418 16417.947
- 147 4029 wm-rh-superiorparietal 11623 11623.260
- 148 4030 wm-rh-superiortemporal 6587 6587.114
- 149 4031 wm-rh-supramarginal 8010 8010.465
- 150 4032 wm-rh-frontalpole 359 359.083
- 151 4033 wm-rh-temporalpole 720 720.218
- 152 4034 wm-rh-transversetemporal 452 452.492
- 153 4035 wm-rh-insula 7547 7546.814
- 154 4100 wm-rh-Unknown 0 0.000
- 155 4101 wm-rh-Corpus_callosum 0 0.000
- 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000
- 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000
- 158 4104 wm-rh-G_cingulate-Main_part 0 0.000
- 159 4105 wm-rh-G_cuneus 0 0.000
- 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000
- 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000
- 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000
- 163 4109 wm-rh-G_frontal_middle 0 0.000
- 164 4110 wm-rh-G_frontal_superior 0 0.000
- 165 4111 wm-rh-G_frontomarginal 0 0.000
- 166 4112 wm-rh-G_insular_long 0 0.000
- 167 4113 wm-rh-G_insular_short 0 0.000
- 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000
- 169 4115 wm-rh-G_occipital_middle 0 0.000
- 170 4116 wm-rh-G_occipital_superior 0 0.000
- 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000
- 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000
- 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000
- 174 4120 wm-rh-G_orbital 0 0.000
- 175 4121 wm-rh-G_paracentral 0 0.000
- 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000
- 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000
- 178 4124 wm-rh-G_parietal_superior 0 0.000
- 179 4125 wm-rh-G_postcentral 0 0.000
- 180 4126 wm-rh-G_precentral 0 0.000
- 181 4127 wm-rh-G_precuneus 0 0.000
- 182 4128 wm-rh-G_rectus 0 0.000
- 183 4129 wm-rh-G_subcallosal 0 0.000
- 184 4130 wm-rh-G_subcentral 0 0.000
- 185 4131 wm-rh-G_temporal_inferior 0 0.000
- 186 4132 wm-rh-G_temporal_middle 0 0.000
- 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000
- 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000
- 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000
- 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000
- 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000
- 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000
- 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000
- 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000
- 195 4141 wm-rh-Medial_wall 0 0.000
- 196 4142 wm-rh-Pole_occipital 0 0.000
- 197 4143 wm-rh-Pole_temporal 0 0.000
- 198 4144 wm-rh-S_calcarine 0 0.000
- 199 4145 wm-rh-S_central 0 0.000
- 200 4146 wm-rh-S_central_insula 0 0.000
- 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000
- 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000
- 203 4149 wm-rh-S_circular_insula_anterior 0 0.000
- 204 4150 wm-rh-S_circular_insula_inferior 0 0.000
- 205 4151 wm-rh-S_circular_insula_superior 0 0.000
- 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000
- 207 4153 wm-rh-S_collateral_transverse_post 0 0.000
- 208 4154 wm-rh-S_frontal_inferior 0 0.000
- 209 4155 wm-rh-S_frontal_middle 0 0.000
- 210 4156 wm-rh-S_frontal_superior 0 0.000
- 211 4157 wm-rh-S_frontomarginal 0 0.000
- 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000
- 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000
- 214 4160 wm-rh-S_occipital_anterior 0 0.000
- 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000
- 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000
- 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000
- 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000
- 219 4165 wm-rh-S_orbital-H_shapped 0 0.000
- 220 4166 wm-rh-S_orbital_lateral 0 0.000
- 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000
- 222 4168 wm-rh-S_paracentral 0 0.000
- 223 4169 wm-rh-S_parieto_occipital 0 0.000
- 224 4170 wm-rh-S_pericallosal 0 0.000
- 225 4171 wm-rh-S_postcentral 0 0.000
- 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000
- 227 4173 wm-rh-S_precentral-Superior-part 0 0.000
- 228 4174 wm-rh-S_subcentral_ant 0 0.000
- 229 4175 wm-rh-S_subcentral_post 0 0.000
- 230 4176 wm-rh-S_suborbital 0 0.000
- 231 4177 wm-rh-S_subparietal 0 0.000
- 232 4178 wm-rh-S_supracingulate 0 0.000
- 233 4179 wm-rh-S_temporal_inferior 0 0.000
- 234 4180 wm-rh-S_temporal_superior 0 0.000
- 235 4181 wm-rh-S_temporal_transverse 0 0.000
- 236 5001 Left-UnsegmentedWhiteMatter 27692 27692.238
- 237 5002 Right-UnsegmentedWhiteMatter 32007 32007.365
- 238 13100 wm_lh_Unknown 0 0.000
- 239 13101 wm_lh_G_and_S_frontomargin 0 0.000
- 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000
- 241 13103 wm_lh_G_and_S_paracentral 0 0.000
- 242 13104 wm_lh_G_and_S_subcentral 0 0.000
- 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000
- 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000
- 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000
- 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000
- 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000
- 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000
- 249 13111 wm_lh_G_cuneus 0 0.000
- 250 13112 wm_lh_G_front_inf-Opercular 0 0.000
- 251 13113 wm_lh_G_front_inf-Orbital 0 0.000
- 252 13114 wm_lh_G_front_inf-Triangul 0 0.000
- 253 13115 wm_lh_G_front_middle 0 0.000
- 254 13116 wm_lh_G_front_sup 0 0.000
- 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000
- 256 13118 wm_lh_G_insular_short 0 0.000
- 257 13119 wm_lh_G_occipital_middle 0 0.000
- 258 13120 wm_lh_G_occipital_sup 0 0.000
- 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000
- 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000
- 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000
- 262 13124 wm_lh_G_orbital 0 0.000
- 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000
- 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000
- 265 13127 wm_lh_G_parietal_sup 0 0.000
- 266 13128 wm_lh_G_postcentral 0 0.000
- 267 13129 wm_lh_G_precentral 0 0.000
- 268 13130 wm_lh_G_precuneus 0 0.000
- 269 13131 wm_lh_G_rectus 0 0.000
- 270 13132 wm_lh_G_subcallosal 0 0.000
- 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000
- 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000
- 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000
- 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000
- 275 13137 wm_lh_G_temporal_inf 0 0.000
- 276 13138 wm_lh_G_temporal_middle 0 0.000
- 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000
- 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000
- 279 13141 wm_lh_Lat_Fis-post 0 0.000
- 280 13142 wm_lh_Medial_wall 0 0.000
- 281 13143 wm_lh_Pole_occipital 0 0.000
- 282 13144 wm_lh_Pole_temporal 0 0.000
- 283 13145 wm_lh_S_calcarine 0 0.000
- 284 13146 wm_lh_S_central 0 0.000
- 285 13147 wm_lh_S_cingul-Marginalis 0 0.000
- 286 13148 wm_lh_S_circular_insula_ant 0 0.000
- 287 13149 wm_lh_S_circular_insula_inf 0 0.000
- 288 13150 wm_lh_S_circular_insula_sup 0 0.000
- 289 13151 wm_lh_S_collat_transv_ant 0 0.000
- 290 13152 wm_lh_S_collat_transv_post 0 0.000
- 291 13153 wm_lh_S_front_inf 0 0.000
- 292 13154 wm_lh_S_front_middle 0 0.000
- 293 13155 wm_lh_S_front_sup 0 0.000
- 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000
- 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000
- 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000
- 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000
- 298 13160 wm_lh_S_occipital_ant 0 0.000
- 299 13161 wm_lh_S_oc-temp_lat 0 0.000
- 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000
- 301 13163 wm_lh_S_orbital_lateral 0 0.000
- 302 13164 wm_lh_S_orbital_med-olfact 0 0.000
- 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000
- 304 13166 wm_lh_S_parieto_occipital 0 0.000
- 305 13167 wm_lh_S_pericallosal 0 0.000
- 306 13168 wm_lh_S_postcentral 0 0.000
- 307 13169 wm_lh_S_precentral-inf-part 0 0.000
- 308 13170 wm_lh_S_precentral-sup-part 0 0.000
- 309 13171 wm_lh_S_suborbital 0 0.000
- 310 13172 wm_lh_S_subparietal 0 0.000
- 311 13173 wm_lh_S_temporal_inf 0 0.000
- 312 13174 wm_lh_S_temporal_sup 0 0.000
- 313 13175 wm_lh_S_temporal_transverse 0 0.000
- 314 14100 wm_rh_Unknown 0 0.000
- 315 14101 wm_rh_G_and_S_frontomargin 0 0.000
- 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000
- 317 14103 wm_rh_G_and_S_paracentral 0 0.000
- 318 14104 wm_rh_G_and_S_subcentral 0 0.000
- 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000
- 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000
- 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000
- 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000
- 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000
- 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000
- 325 14111 wm_rh_G_cuneus 0 0.000
- 326 14112 wm_rh_G_front_inf-Opercular 0 0.000
- 327 14113 wm_rh_G_front_inf-Orbital 0 0.000
- 328 14114 wm_rh_G_front_inf-Triangul 0 0.000
- 329 14115 wm_rh_G_front_middle 0 0.000
- 330 14116 wm_rh_G_front_sup 0 0.000
- 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000
- 332 14118 wm_rh_G_insular_short 0 0.000
- 333 14119 wm_rh_G_occipital_middle 0 0.000
- 334 14120 wm_rh_G_occipital_sup 0 0.000
- 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000
- 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000
- 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000
- 338 14124 wm_rh_G_orbital 0 0.000
- 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000
- 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000
- 341 14127 wm_rh_G_parietal_sup 0 0.000
- 342 14128 wm_rh_G_postcentral 0 0.000
- 343 14129 wm_rh_G_precentral 0 0.000
- 344 14130 wm_rh_G_precuneus 0 0.000
- 345 14131 wm_rh_G_rectus 0 0.000
- 346 14132 wm_rh_G_subcallosal 0 0.000
- 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000
- 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000
- 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000
- 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000
- 351 14137 wm_rh_G_temporal_inf 0 0.000
- 352 14138 wm_rh_G_temporal_middle 0 0.000
- 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000
- 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000
- 355 14141 wm_rh_Lat_Fis-post 0 0.000
- 356 14142 wm_rh_Medial_wall 0 0.000
- 357 14143 wm_rh_Pole_occipital 0 0.000
- 358 14144 wm_rh_Pole_temporal 0 0.000
- 359 14145 wm_rh_S_calcarine 0 0.000
- 360 14146 wm_rh_S_central 0 0.000
- 361 14147 wm_rh_S_cingul-Marginalis 0 0.000
- 362 14148 wm_rh_S_circular_insula_ant 0 0.000
- 363 14149 wm_rh_S_circular_insula_inf 0 0.000
- 364 14150 wm_rh_S_circular_insula_sup 0 0.000
- 365 14151 wm_rh_S_collat_transv_ant 0 0.000
- 366 14152 wm_rh_S_collat_transv_post 0 0.000
- 367 14153 wm_rh_S_front_inf 0 0.000
- 368 14154 wm_rh_S_front_middle 0 0.000
- 369 14155 wm_rh_S_front_sup 0 0.000
- 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000
- 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000
- 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000
- 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000
- 374 14160 wm_rh_S_occipital_ant 0 0.000
- 375 14161 wm_rh_S_oc-temp_lat 0 0.000
- 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000
- 377 14163 wm_rh_S_orbital_lateral 0 0.000
- 378 14164 wm_rh_S_orbital_med-olfact 0 0.000
- 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000
- 380 14166 wm_rh_S_parieto_occipital 0 0.000
- 381 14167 wm_rh_S_pericallosal 0 0.000
- 382 14168 wm_rh_S_postcentral 0 0.000
- 383 14169 wm_rh_S_precentral-inf-part 0 0.000
- 384 14170 wm_rh_S_precentral-sup-part 0 0.000
- 385 14171 wm_rh_S_suborbital 0 0.000
- 386 14172 wm_rh_S_subparietal 0 0.000
- 387 14173 wm_rh_S_temporal_inf 0 0.000
- 388 14174 wm_rh_S_temporal_sup 0 0.000
- 389 14175 wm_rh_S_temporal_transverse 0 0.000
- Reporting on 70 segmentations
- mri_segstats done
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label
- #--------------------------------------------
- #@# BA Labels lh Thu Aug 8 23:11:51 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub004 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA1.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 4129 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4129 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 222
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4351
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub004 --trglabel ./lh.BA2.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA2.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 7909 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 7909 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 480
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8389
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub004 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA3a.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 4077 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4077 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 73
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4150
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub004 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA3b.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 5983 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 5983 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 231
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6214
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub004 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA4a.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 5784 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 5784 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 158
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 5942
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub004 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA4p.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 4070 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4070 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 120
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4190
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub004 --trglabel ./lh.BA6.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA6.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 13589 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 13589 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 869
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 14458
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub004 --trglabel ./lh.BA44.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA44.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 4181 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4181 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 463
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4644
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub004 --trglabel ./lh.BA45.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA45.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 3422 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3422 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 793
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4215
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub004 --trglabel ./lh.V1.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.V1.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 4641 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4641 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 1514
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6155
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub004 --trglabel ./lh.V2.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.V2.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 8114 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 8114 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 3590
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 11704
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub004 --trglabel ./lh.MT.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.MT.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 2018 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 2018 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 611
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2629
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub004 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.perirhinal.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1199 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1199 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 401
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1600
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub004 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA1.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1014 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1014 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 21
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1035
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub004 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA2.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 2092 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 2092 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 187
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2279
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub004 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA3a.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1504 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1504 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 14
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1518
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA3b.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1996 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1996 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 88
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2084
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub004 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA4a.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 2319 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 2319 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 92
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2411
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub004 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA4p.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1549 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1549 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 77
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1626
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub004 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA6.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 7035 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 7035 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 190
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7225
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub004 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA44.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1912 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1912 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 200
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2112
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub004 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.BA45.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1151 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1151 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 299
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1450
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub004 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.V1.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 3405 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3405 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 1018
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4423
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub004 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.V2.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 3334 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3334 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 1627
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 4961
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub004 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./lh.MT.thresh.label
- regmethod = surface
- srchemi = lh
- trghemi = lh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 513 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 513 nlabel points
- Performing mapping from target back to the source label 135159
- Number of reverse mapping hits = 124
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 637
- mri_label2label: Done
- mris_label2annot --s sub004 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose
- Reading ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt
- Number of ctab entries 14
- $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
- cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label
- cmdline mris_label2annot --s sub004 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub004
- hemi lh
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
- AnnotName BA
- nlables 13
- LabelThresh 0 0.000000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.orig
- 1 1530880 BA1
- 2 16749699 BA2
- 3 16711680 BA3a
- 4 3368703 BA3b
- 5 1376196 BA4a
- 6 13382655 BA4p
- 7 10036737 BA6
- 8 2490521 BA44
- 9 39283 BA45
- 10 3993 V1
- 11 8508928 V2
- 12 10027163 MT
- 13 16422433 perirhinal
- Mapping unhit to unknown
- Found 94426 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.BA.annot
- mris_label2annot --s sub004 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- Reading ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt
- Number of ctab entries 14
- $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
- cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label
- cmdline mris_label2annot --s sub004 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub004
- hemi lh
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
- AnnotName BA.thresh
- nlables 12
- LabelThresh 0 0.000000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.orig
- 1 1530880 BA1
- 2 16749699 BA2
- 3 16711680 BA3a
- 4 3368703 BA3b
- 5 1376196 BA4a
- 6 13382655 BA4p
- 7 10036737 BA6
- 8 2490521 BA44
- 9 39283 BA45
- 10 3993 V1
- 11 8508928 V2
- 12 10027163 MT
- Mapping unhit to unknown
- Found 112738 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub004 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- reading colortable from annotation file...
- colortable with 14 entries read (originally /opt/freesurfer/5.3.0/average/colortable_BA.txt)
- Saving annotation colortable ./BA.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 897 543 1493 1.941 0.652 0.158 0.054 21 1.9 BA1
- 4019 2660 7027 2.417 0.500 0.117 0.029 40 4.9 BA2
- 855 562 816 2.006 0.405 0.141 0.048 10 1.5 BA3a
- 2183 1474 3529 2.010 0.621 0.118 0.038 23 3.2 BA3b
- 1384 881 2922 2.815 0.553 0.111 0.028 12 1.6 BA4a
- 1130 748 2190 2.873 0.558 0.103 0.033 8 1.6 BA4p
- 8149 5510 18752 2.724 0.610 0.121 0.033 87 11.1 BA6
- 2321 1559 4789 2.631 0.523 0.122 0.034 29 3.3 BA44
- 3091 2078 6059 2.500 0.525 0.124 0.037 38 4.8 BA45
- 3659 2392 4128 1.732 0.527 0.137 0.056 50 8.6 V1
- 9303 6012 13425 2.062 0.527 0.167 1.235 695 26.5 V2
- 2311 1548 4088 2.520 0.364 0.152 0.050 37 4.4 MT
- 1431 946 4185 3.519 0.616 0.158 0.089 148 6.0 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub004 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- reading colortable from annotation file...
- colortable with 14 entries read (originally /opt/freesurfer/5.3.0/average/colortable_BA.txt)
- Saving annotation colortable ./BA.thresh.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 540 300 802 1.829 0.618 0.167 0.058 13 1.4 BA1
- 1611 1079 3138 2.429 0.517 0.109 0.026 16 1.7 BA2
- 708 469 641 1.989 0.387 0.147 0.051 9 1.4 BA3a
- 1402 961 1817 1.748 0.355 0.094 0.025 8 1.2 BA3b
- 1351 859 2916 2.896 0.545 0.099 0.023 9 1.3 BA4a
- 967 633 1756 2.816 0.571 0.109 0.037 8 1.5 BA4p
- 3941 2667 8959 2.644 0.594 0.121 0.030 43 4.9 BA6
- 1496 998 3105 2.600 0.486 0.118 0.035 21 2.1 BA44
- 1239 834 3048 2.758 0.488 0.135 0.048 21 2.2 BA45
- 3961 2558 4407 1.711 0.525 0.139 0.058 58 9.6 V1
- 4636 3002 5762 1.870 0.454 0.172 2.409 588 14.8 V2
- 569 400 898 2.410 0.383 0.138 0.034 6 0.9 MT
- #--------------------------------------------
- #@# BA Labels rh Thu Aug 8 23:17:45 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub004 --trglabel ./rh.BA1.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA1.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 3962 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3962 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 128
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4090
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub004 --trglabel ./rh.BA2.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA2.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 6687 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 6687 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 188
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 6875
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub004 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA3a.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 3980 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3980 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 80
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4060
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub004 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA3b.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 4522 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4522 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 123
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4645
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub004 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA4a.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 5747 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 5747 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 179
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 5926
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub004 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA4p.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 4473 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4473 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 136
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4609
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub004 --trglabel ./rh.BA6.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA6.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 12256 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 12256 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 550
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 12806
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub004 --trglabel ./rh.BA44.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA44.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 6912 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 6912 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 1049
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 7961
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub004 --trglabel ./rh.BA45.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA45.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 5355 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 5355 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 1383
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6738
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub004 --trglabel ./rh.V1.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.V1.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 4727 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4727 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 1673
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 6400
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub004 --trglabel ./rh.V2.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.V2.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 8016 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 8016 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 3729
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 11745
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub004 --trglabel ./rh.MT.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.MT.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1932 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1932 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 361
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2293
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub004 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.perirhinal.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 752 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 752 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 103
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 855
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub004 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA1.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 876 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 876 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 35
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 911
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub004 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA2.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 2688 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 2688 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 68
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2756
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub004 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA3a.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1698 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1698 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 17
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1715
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub004 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA3b.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 2183 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 2183 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 66
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2249
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub004 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA4a.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1388 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1388 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 64
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1452
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub004 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA4p.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1489 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1489 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 58
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1547
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub004 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA6.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 6959 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 6959 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 282
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7241
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub004 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA44.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1012 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1012 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 246
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1258
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub004 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.BA45.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 1178 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1178 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 264
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1442
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub004 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.V1.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 3232 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3232 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 1088
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4320
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub004 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.V2.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 3437 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3437 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 1809
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 5246
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub004 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface
- srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label
- srcsubject = fsaverage
- trgsubject = sub004
- trglabel = ./rh.MT.thresh.label
- regmethod = surface
- srchemi = rh
- trghemi = rh
- trgsurface = white
- srcsurfreg = sphere.reg
- trgsurfreg = sphere.reg
- usehash = 1
- Use ProjAbs = 0, 0
- Use ProjFrac = 0, 0
- DoPaint 0
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Loading source label.
- Found 268 points in source label.
- Starting surface-based mapping
- Reading source registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 268 nlabel points
- Performing mapping from target back to the source label 134900
- Number of reverse mapping hits = 45
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 313
- mri_label2label: Done
- mris_label2annot --s sub004 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose
- Reading ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt
- Number of ctab entries 14
- $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
- cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label
- cmdline mris_label2annot --s sub004 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub004
- hemi rh
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
- AnnotName BA
- nlables 13
- LabelThresh 0 0.000000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.orig
- 1 1530880 BA1
- 2 16749699 BA2
- 3 16711680 BA3a
- 4 3368703 BA3b
- 5 1376196 BA4a
- 6 13382655 BA4p
- 7 10036737 BA6
- 8 2490521 BA44
- 9 39283 BA45
- 10 3993 V1
- 11 8508928 V2
- 12 10027163 MT
- 13 16422433 perirhinal
- Mapping unhit to unknown
- Found 95117 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.BA.annot
- mris_label2annot --s sub004 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- Reading ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt
- Number of ctab entries 14
- $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
- cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label
- cmdline mris_label2annot --s sub004 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub004
- hemi rh
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
- AnnotName BA.thresh
- nlables 12
- LabelThresh 0 0.000000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.orig
- 1 1530880 BA1
- 2 16749699 BA2
- 3 16711680 BA3a
- 4 3368703 BA3b
- 5 1376196 BA4a
- 6 13382655 BA4p
- 7 10036737 BA6
- 8 2490521 BA44
- 9 39283 BA45
- 10 3993 V1
- 11 8508928 V2
- 12 10027163 MT
- Mapping unhit to unknown
- Found 113489 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub004 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- reading colortable from annotation file...
- colortable with 14 entries read (originally /opt/freesurfer/5.3.0/average/colortable_BA.txt)
- Saving annotation colortable ./BA.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 814 488 2002 2.767 0.446 0.158 0.051 15 1.6 BA1
- 2687 1819 4304 2.253 0.606 0.116 0.031 22 3.4 BA2
- 908 572 765 1.710 0.450 0.142 0.039 10 1.5 BA3a
- 1809 1215 2511 1.679 0.616 0.105 0.028 17 2.1 BA3b
- 1248 740 2712 2.874 0.483 0.118 0.130 48 6.9 BA4a
- 1091 717 1672 2.323 0.487 0.132 0.327 46 4.0 BA4p
- 6303 4189 15779 3.091 0.564 0.132 0.041 79 10.8 BA6
- 4108 2858 7836 2.596 0.559 0.116 0.030 40 4.8 BA44
- 4868 3266 10648 2.747 0.554 0.140 0.046 79 8.8 BA45
- 4003 2636 4914 1.829 0.476 0.155 0.102 182 15.6 V1
- 9357 6113 14105 2.146 0.504 0.164 0.065 188 23.1 V2
- 1911 1271 3021 2.372 0.418 0.147 0.050 28 3.8 MT
- 676 489 2068 3.830 0.782 0.154 0.054 11 1.5 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub004 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- reading colortable from annotation file...
- colortable with 14 entries read (originally /opt/freesurfer/5.3.0/average/colortable_BA.txt)
- Saving annotation colortable ./BA.thresh.ctab
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 550 319 1300 2.660 0.524 0.157 0.049 10 1.1 BA1
- 1567 1059 2565 2.201 0.674 0.109 0.028 11 1.7 BA2
- 781 495 597 1.689 0.402 0.143 0.039 8 1.3 BA3a
- 1424 976 1654 1.497 0.499 0.094 0.023 10 1.4 BA3b
- 779 456 1587 2.967 0.584 0.129 0.143 39 2.6 BA4a
- 882 589 1371 2.371 0.524 0.129 0.110 23 4.3 BA4p
- 4053 2679 10463 3.108 0.576 0.133 0.045 54 7.7 BA6
- 1072 786 2362 2.392 0.644 0.130 0.041 17 1.6 BA44
- 1247 840 2985 2.857 0.453 0.144 0.044 23 2.2 BA45
- 3848 2530 4674 1.825 0.469 0.153 0.103 182 14.8 V1
- 4953 3214 7119 2.096 0.497 0.166 0.068 100 12.9 V2
- 255 186 502 2.393 0.407 0.179 0.066 6 0.7 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Thu Aug 8 23:22:27 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub004 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub004.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.sphere.reg...
- eroding label 1 times before writing
- thresholding label stat at 0.400 before writing
- only 1 subject - copying statistics...
- writing label with 1315 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub004 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 501 340 1420 3.376 0.663 0.124 0.040 4 0.9 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Thu Aug 8 23:22:45 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub004 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub004.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.sphere.reg...
- eroding label 1 times before writing
- thresholding label stat at 0.400 before writing
- only 1 subject - copying statistics...
- writing label with 857 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub004 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- table columns are:
- number of vertices
- total surface area (mm^2)
- total gray matter volume (mm^3)
- average cortical thickness +- standard deviation (mm)
- integrated rectified mean curvature
- integrated rectified Gaussian curvature
- folding index
- intrinsic curvature index
- structure name
- 289 196 848 3.784 0.755 0.131 0.036 2 0.5 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:54:17 CEST 2013
- Ended at Thu Aug 8 23:23:00 CEST 2013
- #@#%# recon-all-run-time-hours 12.479
- recon-all -s sub004 finished without error at Thu Aug 8 23:23:00 CEST 2013
|
