123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696697698699700701702703704705706707708709710711712713714715716717718719720721722723724725726727728729730731732733734735736737738739740741742743744745746747748749750751752753754755756757758759760761762763764765766767768769770771772773774775776777778779780781782783784785786787788789790791792793794795796797798799800801802803804805806807808809810811812813814815816817818819820821822823824825826827828829830831832833834835836837838839840841842843844845846847848849850851852853854855856857858859860861862863864865866867868869870871872873874875876877878879880881882883884885886887888889890891892893894895896897898899900901902903904905906907908909910911912913914915916917918919920921922923924925926927928929930931932933934935936937938939940941942943944945946947948949950951952953954955956957958959960961962963964965966967968969970971972973974975976977978979980981982983984985986987988989990991992993994995996997998999100010011002100310041005100610071008100910101011101210131014101510161017101810191020102110221023102410251026102710281029103010311032103310341035103610371038103910401041104210431044104510461047104810491050105110521053105410551056105710581059106010611062106310641065106610671068106910701071107210731074107510761077107810791080108110821083108410851086108710881089109010911092109310941095109610971098109911001101110211031104110511061107110811091110111111121113111411151116111711181119112011211122112311241125112611271128112911301131113211331134113511361137113811391140114111421143114411451146114711481149115011511152115311541155115611571158115911601161116211631164116511661167116811691170117111721173117411751176117711781179118011811182118311841185118611871188118911901191119211931194119511961197119811991200120112021203120412051206120712081209121012111212121312141215121612171218121912201221122212231224122512261227122812291230123112321233123412351236123712381239124012411242124312441245124612471248124912501251125212531254125512561257125812591260126112621263126412651266126712681269127012711272127312741275127612771278127912801281128212831284128512861287128812891290129112921293129412951296129712981299130013011302130313041305130613071308130913101311131213131314131513161317131813191320132113221323132413251326132713281329133013311332133313341335133613371338133913401341134213431344134513461347134813491350135113521353135413551356135713581359136013611362136313641365136613671368136913701371137213731374137513761377137813791380138113821383138413851386138713881389139013911392139313941395139613971398139914001401140214031404140514061407140814091410141114121413141414151416141714181419142014211422142314241425142614271428142914301431143214331434143514361437143814391440144114421443144414451446144714481449145014511452145314541455145614571458145914601461146214631464146514661467146814691470147114721473147414751476147714781479148014811482148314841485148614871488148914901491149214931494149514961497149814991500150115021503150415051506150715081509151015111512151315141515151615171518151915201521152215231524152515261527152815291530153115321533153415351536153715381539154015411542154315441545154615471548154915501551155215531554155515561557155815591560156115621563156415651566156715681569157015711572157315741575157615771578157915801581158215831584158515861587158815891590159115921593159415951596159715981599160016011602160316041605160616071608160916101611161216131614161516161617161816191620162116221623162416251626162716281629163016311632163316341635163616371638163916401641164216431644164516461647164816491650165116521653165416551656165716581659166016611662166316641665166616671668166916701671167216731674167516761677167816791680168116821683168416851686168716881689169016911692169316941695169616971698169917001701170217031704170517061707170817091710171117121713171417151716171717181719172017211722172317241725172617271728172917301731173217331734173517361737173817391740174117421743174417451746174717481749175017511752175317541755175617571758175917601761176217631764176517661767176817691770177117721773177417751776177717781779178017811782178317841785178617871788178917901791179217931794179517961797179817991800180118021803180418051806180718081809181018111812181318141815181618171818181918201821182218231824182518261827182818291830183118321833183418351836183718381839184018411842184318441845184618471848184918501851185218531854185518561857185818591860186118621863186418651866186718681869187018711872187318741875187618771878187918801881188218831884188518861887188818891890189118921893189418951896189718981899190019011902190319041905190619071908190919101911191219131914191519161917191819191920192119221923192419251926192719281929193019311932193319341935193619371938193919401941194219431944194519461947194819491950195119521953195419551956195719581959196019611962196319641965196619671968196919701971197219731974197519761977197819791980198119821983198419851986198719881989199019911992199319941995199619971998199920002001200220032004200520062007200820092010201120122013201420152016201720182019202020212022202320242025202620272028202920302031203220332034203520362037203820392040204120422043204420452046204720482049205020512052205320542055205620572058205920602061206220632064206520662067206820692070207120722073207420752076207720782079208020812082208320842085208620872088208920902091209220932094209520962097209820992100210121022103210421052106210721082109211021112112211321142115211621172118211921202121212221232124212521262127212821292130213121322133213421352136213721382139214021412142214321442145214621472148214921502151215221532154215521562157215821592160216121622163216421652166216721682169217021712172217321742175217621772178217921802181218221832184218521862187218821892190219121922193219421952196219721982199220022012202220322042205220622072208220922102211221222132214221522162217221822192220222122222223222422252226222722282229223022312232223322342235223622372238223922402241224222432244224522462247224822492250225122522253225422552256225722582259226022612262226322642265226622672268226922702271227222732274227522762277227822792280228122822283228422852286228722882289229022912292229322942295229622972298229923002301230223032304230523062307230823092310231123122313231423152316231723182319232023212322232323242325232623272328232923302331233223332334233523362337233823392340234123422343234423452346234723482349235023512352235323542355235623572358235923602361236223632364236523662367236823692370237123722373237423752376237723782379238023812382238323842385238623872388238923902391239223932394239523962397239823992400240124022403240424052406240724082409241024112412241324142415241624172418241924202421242224232424242524262427242824292430243124322433243424352436243724382439244024412442244324442445244624472448244924502451245224532454245524562457245824592460246124622463246424652466246724682469247024712472247324742475247624772478247924802481248224832484248524862487248824892490249124922493249424952496249724982499250025012502250325042505250625072508250925102511251225132514251525162517251825192520252125222523252425252526252725282529253025312532253325342535253625372538253925402541254225432544254525462547254825492550255125522553255425552556255725582559256025612562256325642565256625672568256925702571257225732574257525762577257825792580258125822583258425852586258725882589259025912592259325942595259625972598259926002601260226032604260526062607260826092610261126122613261426152616261726182619262026212622262326242625262626272628262926302631263226332634263526362637263826392640264126422643264426452646264726482649265026512652265326542655265626572658265926602661266226632664266526662667266826692670267126722673267426752676267726782679268026812682268326842685268626872688268926902691269226932694269526962697269826992700270127022703270427052706270727082709271027112712271327142715271627172718271927202721272227232724272527262727272827292730273127322733273427352736273727382739274027412742274327442745274627472748274927502751275227532754275527562757275827592760276127622763276427652766276727682769277027712772277327742775277627772778277927802781278227832784278527862787278827892790279127922793279427952796279727982799280028012802280328042805280628072808280928102811281228132814281528162817281828192820282128222823282428252826282728282829283028312832283328342835283628372838283928402841284228432844284528462847284828492850285128522853285428552856285728582859286028612862286328642865286628672868286928702871287228732874287528762877287828792880288128822883288428852886288728882889289028912892289328942895289628972898289929002901290229032904290529062907290829092910291129122913291429152916291729182919292029212922292329242925292629272928292929302931293229332934293529362937293829392940294129422943294429452946294729482949295029512952295329542955295629572958295929602961296229632964296529662967296829692970297129722973297429752976297729782979298029812982298329842985298629872988298929902991299229932994299529962997299829993000300130023003300430053006300730083009301030113012301330143015301630173018301930203021302230233024302530263027302830293030303130323033303430353036303730383039304030413042304330443045304630473048304930503051305230533054305530563057305830593060306130623063306430653066306730683069307030713072307330743075307630773078307930803081308230833084308530863087308830893090309130923093309430953096309730983099310031013102310331043105310631073108310931103111311231133114311531163117311831193120312131223123312431253126312731283129313031313132313331343135313631373138313931403141314231433144314531463147314831493150315131523153315431553156315731583159316031613162316331643165316631673168316931703171317231733174317531763177317831793180318131823183318431853186318731883189319031913192319331943195319631973198319932003201320232033204320532063207320832093210321132123213321432153216321732183219322032213222322332243225322632273228322932303231323232333234323532363237323832393240324132423243324432453246324732483249325032513252325332543255325632573258325932603261326232633264326532663267326832693270327132723273327432753276327732783279328032813282328332843285328632873288328932903291329232933294329532963297329832993300330133023303330433053306330733083309331033113312331333143315331633173318331933203321332233233324332533263327332833293330333133323333333433353336333733383339334033413342334333443345334633473348334933503351335233533354335533563357335833593360336133623363336433653366336733683369337033713372337333743375337633773378337933803381338233833384338533863387338833893390339133923393339433953396339733983399340034013402340334043405340634073408340934103411341234133414341534163417341834193420342134223423342434253426342734283429343034313432343334343435343634373438343934403441344234433444344534463447344834493450345134523453345434553456345734583459346034613462346334643465346634673468346934703471347234733474347534763477347834793480348134823483348434853486348734883489349034913492349334943495349634973498349935003501350235033504350535063507350835093510351135123513351435153516351735183519352035213522352335243525352635273528352935303531353235333534353535363537353835393540354135423543354435453546354735483549355035513552355335543555355635573558355935603561356235633564356535663567356835693570357135723573357435753576357735783579358035813582358335843585358635873588358935903591359235933594359535963597359835993600360136023603360436053606360736083609361036113612361336143615361636173618361936203621362236233624362536263627362836293630363136323633363436353636363736383639364036413642364336443645364636473648364936503651365236533654365536563657365836593660366136623663366436653666366736683669367036713672367336743675367636773678367936803681368236833684368536863687368836893690369136923693369436953696369736983699370037013702370337043705370637073708370937103711371237133714371537163717371837193720372137223723372437253726372737283729373037313732373337343735373637373738373937403741374237433744374537463747374837493750375137523753375437553756375737583759376037613762376337643765376637673768376937703771377237733774377537763777377837793780378137823783378437853786378737883789379037913792379337943795379637973798379938003801380238033804380538063807380838093810381138123813381438153816381738183819382038213822382338243825382638273828382938303831383238333834383538363837383838393840384138423843384438453846384738483849385038513852385338543855385638573858385938603861386238633864386538663867386838693870387138723873387438753876387738783879388038813882388338843885388638873888388938903891389238933894389538963897389838993900390139023903390439053906390739083909391039113912391339143915391639173918391939203921392239233924392539263927392839293930393139323933393439353936393739383939394039413942394339443945394639473948394939503951395239533954395539563957395839593960396139623963396439653966396739683969397039713972397339743975397639773978397939803981398239833984398539863987398839893990399139923993399439953996399739983999400040014002400340044005400640074008400940104011401240134014401540164017401840194020402140224023402440254026402740284029403040314032403340344035403640374038403940404041404240434044404540464047404840494050405140524053405440554056405740584059406040614062406340644065406640674068406940704071407240734074407540764077407840794080408140824083408440854086408740884089409040914092409340944095409640974098409941004101410241034104410541064107410841094110411141124113411441154116411741184119412041214122412341244125412641274128412941304131413241334134413541364137413841394140414141424143414441454146414741484149415041514152415341544155415641574158415941604161416241634164416541664167416841694170417141724173417441754176417741784179418041814182418341844185418641874188418941904191419241934194419541964197419841994200420142024203420442054206420742084209421042114212421342144215421642174218421942204221422242234224422542264227422842294230423142324233423442354236423742384239424042414242424342444245424642474248424942504251425242534254425542564257425842594260426142624263426442654266426742684269427042714272427342744275427642774278427942804281428242834284428542864287428842894290429142924293429442954296429742984299430043014302430343044305430643074308430943104311431243134314431543164317431843194320432143224323432443254326432743284329433043314332433343344335433643374338433943404341434243434344434543464347434843494350435143524353435443554356435743584359436043614362436343644365436643674368436943704371437243734374437543764377437843794380438143824383438443854386438743884389439043914392439343944395439643974398439944004401440244034404440544064407440844094410441144124413441444154416441744184419442044214422442344244425442644274428442944304431443244334434443544364437443844394440444144424443444444454446444744484449445044514452445344544455445644574458445944604461446244634464446544664467446844694470447144724473447444754476447744784479448044814482448344844485448644874488448944904491449244934494449544964497449844994500450145024503450445054506450745084509451045114512451345144515451645174518451945204521452245234524452545264527452845294530453145324533453445354536453745384539454045414542454345444545454645474548454945504551455245534554455545564557455845594560456145624563456445654566456745684569457045714572457345744575457645774578457945804581458245834584458545864587458845894590459145924593459445954596459745984599460046014602460346044605460646074608460946104611461246134614461546164617461846194620462146224623462446254626462746284629463046314632463346344635463646374638463946404641464246434644464546464647464846494650465146524653465446554656465746584659466046614662466346644665466646674668466946704671467246734674467546764677467846794680468146824683468446854686468746884689469046914692469346944695469646974698469947004701470247034704470547064707470847094710471147124713471447154716471747184719472047214722472347244725472647274728472947304731473247334734473547364737473847394740474147424743474447454746474747484749475047514752475347544755475647574758475947604761476247634764476547664767476847694770477147724773477447754776477747784779478047814782478347844785478647874788478947904791479247934794479547964797479847994800480148024803480448054806480748084809481048114812481348144815481648174818481948204821482248234824482548264827482848294830483148324833483448354836483748384839484048414842484348444845484648474848484948504851485248534854485548564857485848594860486148624863486448654866486748684869487048714872487348744875487648774878487948804881488248834884488548864887488848894890489148924893489448954896489748984899490049014902490349044905490649074908490949104911491249134914491549164917491849194920492149224923492449254926492749284929493049314932493349344935493649374938493949404941494249434944494549464947494849494950495149524953495449554956495749584959496049614962496349644965496649674968496949704971497249734974497549764977497849794980498149824983498449854986498749884989499049914992499349944995499649974998499950005001500250035004500550065007500850095010501150125013501450155016501750185019502050215022502350245025502650275028502950305031503250335034503550365037503850395040504150425043504450455046504750485049505050515052505350545055505650575058505950605061506250635064506550665067506850695070507150725073507450755076507750785079508050815082508350845085508650875088508950905091509250935094509550965097509850995100510151025103510451055106510751085109511051115112511351145115511651175118511951205121512251235124512551265127512851295130513151325133513451355136513751385139514051415142514351445145514651475148514951505151515251535154515551565157515851595160516151625163516451655166516751685169517051715172517351745175517651775178517951805181518251835184518551865187518851895190519151925193519451955196519751985199520052015202520352045205520652075208520952105211521252135214521552165217521852195220522152225223522452255226522752285229523052315232523352345235523652375238523952405241524252435244524552465247524852495250525152525253525452555256525752585259526052615262526352645265526652675268526952705271527252735274527552765277527852795280528152825283528452855286528752885289529052915292529352945295529652975298529953005301530253035304530553065307530853095310531153125313531453155316531753185319532053215322532353245325532653275328532953305331533253335334533553365337533853395340534153425343534453455346534753485349535053515352535353545355535653575358535953605361536253635364536553665367536853695370537153725373537453755376537753785379538053815382538353845385538653875388538953905391539253935394539553965397539853995400540154025403540454055406540754085409541054115412541354145415541654175418541954205421542254235424542554265427542854295430543154325433543454355436543754385439544054415442544354445445544654475448544954505451545254535454545554565457545854595460546154625463546454655466546754685469547054715472547354745475547654775478547954805481548254835484548554865487548854895490549154925493549454955496549754985499550055015502550355045505550655075508550955105511551255135514551555165517551855195520552155225523552455255526552755285529553055315532553355345535553655375538553955405541554255435544554555465547554855495550555155525553555455555556555755585559556055615562556355645565556655675568556955705571557255735574557555765577557855795580558155825583558455855586558755885589559055915592559355945595559655975598559956005601560256035604560556065607560856095610561156125613561456155616561756185619562056215622562356245625562656275628562956305631563256335634563556365637563856395640564156425643564456455646564756485649565056515652565356545655565656575658565956605661566256635664566556665667566856695670567156725673567456755676567756785679568056815682568356845685568656875688568956905691569256935694569556965697569856995700570157025703570457055706570757085709571057115712571357145715571657175718571957205721572257235724572557265727572857295730573157325733573457355736573757385739574057415742574357445745574657475748574957505751575257535754575557565757575857595760576157625763576457655766576757685769577057715772577357745775577657775778577957805781578257835784578557865787578857895790579157925793579457955796579757985799580058015802580358045805580658075808580958105811581258135814581558165817581858195820582158225823582458255826582758285829583058315832583358345835583658375838583958405841584258435844584558465847584858495850585158525853585458555856585758585859586058615862586358645865586658675868586958705871587258735874587558765877587858795880588158825883588458855886588758885889589058915892589358945895589658975898589959005901590259035904590559065907590859095910591159125913591459155916591759185919592059215922592359245925592659275928592959305931593259335934593559365937593859395940594159425943594459455946594759485949595059515952595359545955595659575958595959605961596259635964596559665967596859695970597159725973597459755976597759785979598059815982598359845985598659875988598959905991599259935994599559965997599859996000600160026003600460056006600760086009601060116012601360146015601660176018601960206021602260236024602560266027602860296030603160326033603460356036603760386039604060416042604360446045604660476048604960506051605260536054605560566057605860596060606160626063606460656066606760686069607060716072607360746075607660776078607960806081608260836084608560866087608860896090609160926093609460956096609760986099610061016102610361046105610661076108610961106111611261136114611561166117611861196120612161226123612461256126612761286129613061316132613361346135613661376138613961406141614261436144614561466147614861496150615161526153615461556156615761586159616061616162616361646165616661676168616961706171617261736174617561766177617861796180618161826183618461856186618761886189619061916192619361946195619661976198619962006201620262036204620562066207620862096210621162126213621462156216621762186219622062216222622362246225622662276228622962306231623262336234623562366237623862396240624162426243624462456246624762486249625062516252625362546255625662576258625962606261626262636264626562666267626862696270627162726273627462756276627762786279628062816282628362846285628662876288628962906291629262936294629562966297629862996300630163026303630463056306630763086309631063116312631363146315631663176318631963206321632263236324632563266327632863296330633163326333633463356336633763386339634063416342634363446345634663476348634963506351635263536354635563566357635863596360636163626363636463656366636763686369637063716372637363746375637663776378637963806381638263836384638563866387638863896390639163926393639463956396639763986399640064016402640364046405640664076408640964106411641264136414641564166417641864196420642164226423642464256426642764286429643064316432643364346435643664376438643964406441644264436444644564466447644864496450645164526453645464556456645764586459646064616462646364646465646664676468646964706471647264736474647564766477647864796480648164826483648464856486648764886489649064916492649364946495649664976498649965006501650265036504650565066507650865096510651165126513651465156516651765186519652065216522652365246525652665276528652965306531653265336534653565366537653865396540654165426543654465456546654765486549655065516552655365546555655665576558655965606561656265636564656565666567656865696570657165726573657465756576657765786579658065816582658365846585658665876588658965906591659265936594659565966597659865996600660166026603660466056606660766086609661066116612661366146615661666176618661966206621662266236624662566266627662866296630663166326633663466356636663766386639664066416642664366446645664666476648664966506651665266536654665566566657665866596660666166626663666466656666666766686669667066716672667366746675667666776678667966806681668266836684668566866687668866896690669166926693669466956696669766986699670067016702670367046705670667076708670967106711671267136714671567166717671867196720672167226723672467256726672767286729673067316732673367346735673667376738673967406741674267436744674567466747674867496750675167526753675467556756675767586759676067616762676367646765676667676768676967706771677267736774677567766777677867796780678167826783678467856786678767886789679067916792679367946795679667976798679968006801680268036804680568066807680868096810681168126813681468156816681768186819682068216822682368246825682668276828682968306831683268336834683568366837683868396840684168426843684468456846684768486849685068516852685368546855685668576858685968606861686268636864686568666867686868696870687168726873687468756876687768786879688068816882688368846885688668876888688968906891689268936894689568966897689868996900690169026903690469056906690769086909691069116912691369146915691669176918691969206921692269236924692569266927692869296930693169326933693469356936693769386939694069416942694369446945694669476948694969506951695269536954695569566957695869596960696169626963696469656966696769686969697069716972697369746975697669776978697969806981698269836984698569866987698869896990699169926993699469956996699769986999700070017002700370047005700670077008700970107011701270137014701570167017701870197020702170227023702470257026702770287029703070317032703370347035703670377038703970407041704270437044704570467047704870497050705170527053705470557056705770587059706070617062706370647065706670677068706970707071707270737074707570767077707870797080708170827083708470857086708770887089709070917092709370947095709670977098709971007101710271037104710571067107710871097110711171127113711471157116711771187119712071217122712371247125712671277128712971307131713271337134713571367137713871397140714171427143714471457146714771487149715071517152715371547155715671577158715971607161716271637164716571667167716871697170717171727173717471757176717771787179718071817182718371847185718671877188718971907191719271937194719571967197719871997200720172027203720472057206720772087209721072117212721372147215721672177218721972207221722272237224722572267227722872297230723172327233723472357236723772387239724072417242724372447245724672477248724972507251725272537254725572567257725872597260726172627263726472657266726772687269727072717272727372747275727672777278727972807281728272837284728572867287728872897290729172927293729472957296729772987299730073017302730373047305730673077308730973107311731273137314731573167317731873197320732173227323732473257326732773287329733073317332733373347335733673377338733973407341734273437344734573467347734873497350735173527353735473557356735773587359736073617362736373647365736673677368736973707371737273737374737573767377737873797380738173827383738473857386738773887389739073917392739373947395739673977398739974007401740274037404740574067407740874097410741174127413741474157416741774187419742074217422742374247425742674277428742974307431743274337434743574367437743874397440744174427443744474457446744774487449745074517452745374547455745674577458745974607461746274637464746574667467746874697470747174727473747474757476747774787479748074817482748374847485748674877488748974907491749274937494749574967497749874997500750175027503750475057506750775087509751075117512751375147515751675177518751975207521752275237524752575267527752875297530753175327533753475357536753775387539754075417542754375447545754675477548754975507551755275537554755575567557755875597560756175627563756475657566756775687569757075717572757375747575757675777578757975807581758275837584758575867587758875897590759175927593759475957596759775987599760076017602760376047605760676077608760976107611761276137614761576167617761876197620762176227623762476257626762776287629763076317632763376347635763676377638763976407641764276437644764576467647764876497650765176527653765476557656765776587659766076617662766376647665766676677668766976707671767276737674767576767677767876797680768176827683768476857686768776887689769076917692769376947695769676977698769977007701770277037704770577067707770877097710771177127713771477157716771777187719772077217722772377247725772677277728772977307731773277337734773577367737773877397740774177427743774477457746774777487749775077517752775377547755775677577758775977607761776277637764776577667767776877697770777177727773777477757776777777787779778077817782778377847785778677877788778977907791779277937794779577967797779877997800780178027803780478057806780778087809781078117812781378147815781678177818781978207821782278237824782578267827782878297830783178327833783478357836783778387839784078417842784378447845784678477848784978507851785278537854785578567857785878597860786178627863786478657866786778687869787078717872787378747875787678777878787978807881788278837884788578867887788878897890789178927893789478957896789778987899790079017902790379047905790679077908790979107911791279137914791579167917791879197920792179227923792479257926792779287929793079317932793379347935793679377938793979407941794279437944794579467947794879497950795179527953795479557956795779587959796079617962796379647965796679677968796979707971797279737974797579767977797879797980798179827983798479857986798779887989799079917992799379947995799679977998799980008001800280038004800580068007800880098010801180128013801480158016801780188019802080218022802380248025802680278028802980308031803280338034803580368037803880398040804180428043804480458046804780488049805080518052805380548055805680578058805980608061806280638064806580668067806880698070807180728073807480758076807780788079808080818082808380848085808680878088808980908091809280938094809580968097809880998100810181028103810481058106810781088109811081118112811381148115811681178118811981208121812281238124812581268127812881298130813181328133813481358136813781388139814081418142814381448145814681478148814981508151815281538154815581568157815881598160816181628163816481658166816781688169817081718172817381748175817681778178817981808181818281838184818581868187818881898190819181928193819481958196819781988199820082018202820382048205820682078208820982108211821282138214821582168217821882198220822182228223822482258226822782288229823082318232823382348235823682378238823982408241824282438244824582468247824882498250825182528253825482558256825782588259826082618262826382648265826682678268826982708271827282738274827582768277827882798280828182828283828482858286828782888289829082918292829382948295829682978298829983008301830283038304830583068307830883098310831183128313831483158316831783188319832083218322832383248325832683278328832983308331833283338334833583368337833883398340834183428343834483458346834783488349835083518352835383548355835683578358835983608361836283638364836583668367836883698370837183728373837483758376837783788379838083818382838383848385838683878388838983908391839283938394839583968397839883998400840184028403840484058406840784088409841084118412841384148415841684178418841984208421842284238424842584268427842884298430843184328433843484358436843784388439844084418442844384448445844684478448844984508451845284538454845584568457845884598460846184628463846484658466846784688469847084718472847384748475847684778478847984808481848284838484848584868487848884898490849184928493849484958496849784988499850085018502850385048505850685078508850985108511851285138514851585168517851885198520852185228523852485258526852785288529853085318532853385348535853685378538853985408541854285438544854585468547854885498550855185528553855485558556855785588559856085618562856385648565856685678568856985708571857285738574857585768577857885798580858185828583858485858586858785888589859085918592859385948595859685978598859986008601860286038604860586068607860886098610861186128613861486158616861786188619862086218622862386248625862686278628862986308631863286338634863586368637863886398640864186428643864486458646864786488649865086518652865386548655865686578658865986608661866286638664866586668667866886698670867186728673867486758676867786788679868086818682868386848685868686878688868986908691869286938694869586968697869886998700870187028703870487058706870787088709871087118712871387148715871687178718871987208721872287238724872587268727872887298730873187328733873487358736873787388739874087418742874387448745874687478748874987508751875287538754875587568757875887598760876187628763876487658766876787688769877087718772877387748775877687778778877987808781878287838784878587868787878887898790879187928793879487958796879787988799880088018802880388048805880688078808880988108811881288138814881588168817881888198820882188228823882488258826882788288829883088318832883388348835883688378838883988408841884288438844884588468847884888498850885188528853885488558856885788588859886088618862886388648865886688678868886988708871887288738874887588768877887888798880888188828883888488858886888788888889889088918892889388948895889688978898889989008901890289038904890589068907890889098910891189128913891489158916891789188919892089218922892389248925892689278928892989308931893289338934893589368937893889398940894189428943894489458946894789488949895089518952895389548955895689578958895989608961896289638964896589668967896889698970897189728973897489758976897789788979898089818982898389848985898689878988898989908991899289938994899589968997899889999000900190029003900490059006900790089009901090119012901390149015901690179018901990209021902290239024902590269027902890299030903190329033903490359036903790389039904090419042904390449045904690479048904990509051905290539054905590569057905890599060906190629063906490659066906790689069907090719072907390749075907690779078907990809081908290839084908590869087908890899090909190929093909490959096909790989099910091019102910391049105910691079108910991109111911291139114911591169117911891199120912191229123912491259126912791289129913091319132913391349135913691379138913991409141914291439144914591469147914891499150915191529153915491559156915791589159916091619162916391649165916691679168916991709171917291739174917591769177917891799180918191829183918491859186918791889189919091919192919391949195919691979198919992009201920292039204920592069207920892099210921192129213921492159216921792189219922092219222922392249225922692279228922992309231923292339234923592369237923892399240924192429243924492459246924792489249925092519252925392549255925692579258925992609261926292639264926592669267926892699270927192729273927492759276927792789279928092819282928392849285928692879288928992909291929292939294929592969297929892999300930193029303930493059306930793089309931093119312931393149315931693179318931993209321932293239324932593269327932893299330933193329333933493359336933793389339934093419342934393449345934693479348934993509351935293539354935593569357935893599360936193629363936493659366936793689369937093719372937393749375937693779378937993809381938293839384938593869387938893899390939193929393939493959396939793989399940094019402940394049405940694079408940994109411941294139414941594169417941894199420942194229423942494259426942794289429943094319432943394349435943694379438943994409441944294439444944594469447944894499450945194529453945494559456945794589459946094619462946394649465946694679468946994709471947294739474947594769477947894799480948194829483948494859486948794889489949094919492949394949495949694979498949995009501950295039504950595069507950895099510951195129513951495159516951795189519952095219522952395249525952695279528952995309531953295339534953595369537953895399540954195429543954495459546954795489549955095519552955395549555955695579558955995609561956295639564956595669567956895699570957195729573957495759576957795789579958095819582958395849585958695879588958995909591959295939594959595969597959895999600960196029603960496059606960796089609961096119612961396149615961696179618961996209621962296239624962596269627962896299630963196329633963496359636963796389639964096419642964396449645964696479648964996509651965296539654965596569657965896599660966196629663966496659666966796689669967096719672967396749675967696779678967996809681968296839684968596869687968896899690969196929693969496959696969796989699970097019702970397049705970697079708970997109711971297139714971597169717971897199720972197229723972497259726972797289729973097319732973397349735973697379738973997409741974297439744974597469747974897499750975197529753975497559756975797589759976097619762976397649765976697679768976997709771977297739774977597769777977897799780978197829783978497859786978797889789979097919792979397949795979697979798979998009801980298039804980598069807980898099810981198129813981498159816981798189819982098219822982398249825982698279828982998309831983298339834983598369837983898399840984198429843984498459846984798489849985098519852985398549855985698579858985998609861986298639864986598669867986898699870987198729873987498759876987798789879988098819882988398849885988698879888988998909891989298939894989598969897989898999900990199029903990499059906990799089909991099119912991399149915991699179918991999209921992299239924992599269927992899299930993199329933993499359936993799389939994099419942994399449945994699479948994999509951995299539954995599569957995899599960996199629963996499659966996799689969997099719972997399749975997699779978997999809981998299839984998599869987998899899990999199929993999499959996999799989999100001000110002100031000410005100061000710008100091001010011100121001310014100151001610017100181001910020100211002210023100241002510026100271002810029100301003110032100331003410035100361003710038100391004010041100421004310044100451004610047100481004910050100511005210053100541005510056100571005810059100601006110062100631006410065100661006710068100691007010071100721007310074100751007610077100781007910080100811008210083100841008510086100871008810089100901009110092100931009410095100961009710098100991010010101101021010310104101051010610107101081010910110101111011210113101141011510116101171011810119101201012110122101231012410125101261012710128101291013010131101321013310134101351013610137101381013910140101411014210143101441014510146101471014810149101501015110152101531015410155101561015710158101591016010161101621016310164101651016610167101681016910170101711017210173101741017510176101771017810179101801018110182101831018410185101861018710188101891019010191101921019310194101951019610197101981019910200102011020210203102041020510206102071020810209102101021110212102131021410215102161021710218102191022010221102221022310224102251022610227102281022910230102311023210233102341023510236102371023810239102401024110242102431024410245102461024710248102491025010251102521025310254102551025610257102581025910260102611026210263102641026510266102671026810269102701027110272102731027410275102761027710278102791028010281102821028310284102851028610287102881028910290102911029210293102941029510296102971029810299103001030110302103031030410305103061030710308103091031010311103121031310314103151031610317103181031910320103211032210323103241032510326103271032810329103301033110332103331033410335103361033710338103391034010341103421034310344103451034610347103481034910350103511035210353103541035510356103571035810359103601036110362103631036410365103661036710368103691037010371103721037310374103751037610377103781037910380103811038210383103841038510386103871038810389103901039110392103931039410395103961039710398103991040010401104021040310404104051040610407104081040910410104111041210413104141041510416104171041810419104201042110422104231042410425104261042710428104291043010431104321043310434104351043610437104381043910440104411044210443104441044510446104471044810449104501045110452104531045410455104561045710458104591046010461104621046310464104651046610467104681046910470104711047210473104741047510476104771047810479104801048110482104831048410485104861048710488104891049010491104921049310494104951049610497104981049910500105011050210503105041050510506105071050810509105101051110512105131051410515105161051710518105191052010521105221052310524105251052610527105281052910530105311053210533105341053510536105371053810539105401054110542105431054410545105461054710548105491055010551105521055310554105551055610557105581055910560105611056210563105641056510566105671056810569105701057110572105731057410575105761057710578105791058010581105821058310584105851058610587105881058910590105911059210593105941059510596105971059810599106001060110602106031060410605106061060710608106091061010611106121061310614106151061610617106181061910620106211062210623106241062510626106271062810629106301063110632106331063410635106361063710638106391064010641106421064310644106451064610647106481064910650106511065210653106541065510656106571065810659106601066110662106631066410665106661066710668106691067010671106721067310674106751067610677106781067910680106811068210683106841068510686106871068810689106901069110692106931069410695106961069710698106991070010701107021070310704107051070610707107081070910710107111071210713107141071510716107171071810719107201072110722107231072410725107261072710728107291073010731107321073310734107351073610737107381073910740107411074210743107441074510746107471074810749107501075110752107531075410755107561075710758107591076010761107621076310764107651076610767107681076910770107711077210773107741077510776107771077810779107801078110782107831078410785107861078710788107891079010791 |
- Thu Aug 8 10:53:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz -T2pial -subjid sub006 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub006
- 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 96468108 2733584 0 177872 94401912
- -/+ buffers/cache: 1888324 97313368
- 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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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/sub006
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998757, 0.0408089, 0.02861)
- j_ras = (0.0441177, 0.99097, 0.126615)
- k_ras = (0.0231846, -0.12772, 0.991539)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998757, 0.0408089, 0.02861)
- j_ras = (0.0441177, 0.99097, 0.126615)
- k_ras = (0.0231846, -0.12772, 0.991539)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:33 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998757, 0.0408089, 0.02861)
- j_ras = (0.0441177, 0.99097, 0.126615)
- k_ras = (0.0231846, -0.12772, 0.991539)
- Original Data has (0.699921, 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/sub006/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 10:58:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6592, pval=0.3663 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach_avi.log
- TalAviQA: 0.96493
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:58:11 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/sub006/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 10:58:11 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.12861
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12861/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12861/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, -1.16415e-09, 1.86265e-09)
- j_ras = (-1.86265e-09, 1.49012e-08, -1)
- k_ras = (9.31323e-10, 1, -1.49012e-08)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.12861/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:14 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.12861/nu0.mnc ./tmp.mri_nu_correct.mni.12861/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12861/0/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:58:14] 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.12861/0/ ./tmp.mri_nu_correct.mni.12861/nu0.mnc ./tmp.mri_nu_correct.mni.12861/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
- Number of iterations: 25
- CV of field change: 0.000992595
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:58:53] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12861/nu0.mnc ./tmp.mri_nu_correct.mni.12861/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:59:01 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.12861/nu1.mnc ./tmp.mri_nu_correct.mni.12861/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12861/1/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:59:01] 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.12861/1/ ./tmp.mri_nu_correct.mni.12861/nu1.mnc ./tmp.mri_nu_correct.mni.12861/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
- Number of iterations: 22
- CV of field change: 0.000982201
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:59:39] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12861/nu1.mnc ./tmp.mri_nu_correct.mni.12861/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12861/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/sub006/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12861/ones.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.12861/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.12861/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.12861/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/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.12861/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/input.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.12861/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.12861/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12861/ones.mgz --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/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.12861/ones.mgz --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/output.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.12861/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.12861/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.12861/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.12861/nu2.mnc ./tmp.mri_nu_correct.mni.12861/nu2.mnc mul .95246908919991135291
- Saving result to './tmp.mri_nu_correct.mni.12861/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.12861/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.12861/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.12861/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.16415e-09, 1.86265e-09)
- j_ras = (-1.86265e-09, 1.49012e-08, -1)
- k_ras = (9.31323e-10, 1, -1.49012e-08)
- 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 (12, 169) to ( 3, 110)
-
-
- Thu Aug 8 11:00:31 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:00:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.130 -0.028 0.007 3.552;
- 0.019 0.978 0.305 -29.156;
- -0.010 -0.429 1.099 -5.547;
- 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 = 19
- Starting OpenSpline(): npoints = 19
- 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 108
- gm peak at 48 (48), valley at 37 (37)
- csf peak at 12, setting threshold to 36
- 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 49 (49), valley at 38 (38)
- csf peak at 12, setting threshold to 36
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 52 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:03:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = (49, 0, 9) --> (203, 255, 206)
- using (100, 85, 108) as brain centroid...
- mean wm in atlas = 126, using box (81,53,84) --> (118, 116,132) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 110, scaling input intensities by 1.145
- scaling channel 0 by 1.14545
- initial log_p = -4.8
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.579503 @ (-9.091, 27.273, -9.091)
- max log p = -4.430745 @ (4.545, -4.545, -4.545)
- max log p = -4.333447 @ (2.273, 2.273, 2.273)
- max log p = -4.291113 @ (1.136, -3.409, 3.409)
- max log p = -4.289512 @ (0.568, 0.568, -0.568)
- max log p = -4.289512 @ (0.000, 0.000, 0.000)
- Found translation: (-0.6, 22.2, -8.5): log p = -4.290
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.3 (thresh=-4.3)
- 1.150 0.000 0.000 -19.518;
- 0.000 1.111 0.298 -22.904;
- 0.000 -0.220 0.821 33.748;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.150 0.000 0.000 -19.518;
- 0.000 1.148 0.450 -36.545;
- 0.000 -0.426 0.965 37.642;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.150 0.000 0.000 -19.518;
- 0.000 1.148 0.450 -36.545;
- 0.000 -0.426 0.965 37.642;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.150 0.000 0.000 -19.518;
- 0.000 1.195 0.393 -36.297;
- 0.000 -0.343 0.973 28.950;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.150 0.000 0.000 -19.518;
- 0.000 1.195 0.393 -36.297;
- 0.000 -0.343 0.973 28.950;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.152 -0.014 -0.022 -16.911;
- 0.019 1.193 0.401 -40.410;
- 0.019 -0.352 0.968 27.618;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.150 -0.014 -0.022 -16.577;
- 0.019 1.196 0.402 -40.788;
- 0.019 -0.351 0.967 27.711;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.150 -0.014 -0.022 -16.577;
- 0.019 1.196 0.402 -40.788;
- 0.019 -0.351 0.967 27.711;
- 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
- 1.14969 -0.01394 -0.02235 -16.57664;
- 0.01903 1.19625 0.40165 -40.78821;
- 0.01860 -0.35144 0.96652 27.71052;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.14969 -0.01394 -0.02235 -16.57664;
- 0.01903 1.19625 0.40165 -40.78821;
- 0.01860 -0.35144 0.96652 27.71052;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.150 -0.014 -0.022 -16.577;
- 0.019 1.196 0.402 -40.788;
- 0.019 -0.351 0.967 27.711;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.8)
- transform before final EM align:
- 1.150 -0.014 -0.022 -16.577;
- 0.019 1.196 0.402 -40.788;
- 0.019 -0.351 0.967 27.711;
- 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
- 1.14969 -0.01394 -0.02235 -16.57664;
- 0.01903 1.19625 0.40165 -40.78821;
- 0.01860 -0.35144 0.96652 27.71052;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.14969 -0.01394 -0.02235 -16.57664;
- 0.01903 1.19625 0.40165 -40.78821;
- 0.01860 -0.35144 0.96652 27.71052;
- 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: 012: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.150 -0.014 -0.022 -16.577;
- 0.019 1.196 0.402 -40.788;
- 0.019 -0.351 0.967 27.711;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 40 minutes and 23 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=128 y=85 z=117 r=94
- first estimation of the main basin volume: 3486435 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 16 found in the rest of the brain
- global maximum in x=147, y=83, z=76, Imax=255
- CSF=13, 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=20180669030 voxels, voxel volume =1.000
- = 20180669030 mmm3 = 20180668.416 cm3
- done.
- PostAnalyze...Basin Prior
- 129 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=94, z=110, r=11272 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45874
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1031766979
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1091834324
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073225896
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1082017464
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1069711904
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 4, 5, 24, 49
- after analyzing : 4, 18, 25, 25
- RIGHT_CER
- before analyzing : 4, 4, 19, 50
- after analyzing : 4, 18, 25, 26
- LEFT_CER
- before analyzing : 4, 4, 20, 51
- after analyzing : 4, 18, 25, 26
- RIGHT_BRAIN
- before analyzing : 4, 5, 24, 49
- after analyzing : 4, 18, 25, 25
- LEFT_BRAIN
- before analyzing : 4, 5, 24, 45
- after analyzing : 4, 18, 25, 24
- OTHER
- before analyzing : 24, 55, 79, 95
- after analyzing : 24, 71, 79, 77
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...70 iterations
- *********************VALIDATION*********************
- curvature mean = -0.012, std = 0.011
- curvature mean = 74.901, std = 9.916
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 1.94, sigma = 3.55
- after rotation: sse = 1.94, sigma = 3.55
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 2.15, its var is 3.63
- before Erosion-Dilatation 0.50% 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...47 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 2061870 voxels, voxel volume = 1.000 mm3
- = 2061870 mmm3 = 2061.870 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:44:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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=20.0
- skull bounding box = (58, 30, 25) --> (194, 179, 204)
- using (103, 80, 115) as brain centroid...
- mean wm in atlas = 107, using box (86,62,93) --> (119, 98,137) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 109, scaling input intensities by 0.982
- scaling channel 0 by 0.981651
- initial log_p = -4.5
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.122993 @ (-9.091, 27.273, -9.091)
- max log p = -3.901602 @ (4.545, -4.545, 4.545)
- max log p = -3.831934 @ (2.273, -2.273, -2.273)
- max log p = -3.790007 @ (-1.136, 1.136, -1.136)
- max log p = -3.768490 @ (0.568, -0.568, -0.568)
- max log p = -3.768490 @ (0.000, 0.000, 0.000)
- Found translation: (-2.8, 21.0, -8.5): log p = -3.768
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.8 (thresh=-3.8)
- 1.075 0.000 0.000 -12.565;
- 0.000 1.028 0.275 -5.513;
- 0.000 -0.236 0.883 27.980;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 1.075 0.000 0.000 -12.565;
- 0.000 1.028 0.275 -5.513;
- 0.000 -0.236 0.883 27.980;
- 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=-3.3, old_max_log_p =-3.4 (thresh=-3.4)
- 1.074 0.026 0.039 -17.352;
- -0.034 1.038 0.307 -9.231;
- -0.035 -0.266 0.856 40.123;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.054 0.025 0.038 -14.649;
- -0.034 1.038 0.307 -9.231;
- -0.035 -0.266 0.856 40.123;
- 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=-3.2, old_max_log_p =-3.3 (thresh=-3.3)
- 1.057 0.021 0.022 -13.719;
- -0.025 1.045 0.279 -8.970;
- -0.018 -0.231 0.863 32.977;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.057 0.021 0.022 -13.719;
- -0.025 1.044 0.279 -8.820;
- -0.018 -0.231 0.863 32.977;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.057 0.021 0.022 -13.719;
- -0.025 1.044 0.279 -8.820;
- -0.018 -0.231 0.863 32.977;
- 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
- 1.05686 0.02056 0.02170 -13.71878;
- -0.02464 1.04352 0.27875 -8.82042;
- -0.01831 -0.23067 0.86304 32.97652;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.05686 0.02056 0.02170 -13.71878;
- -0.02464 1.04352 0.27875 -8.82042;
- -0.01831 -0.23067 0.86304 32.97652;
- 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: 009: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.057 0.021 0.022 -13.719;
- -0.025 1.044 0.279 -8.820;
- -0.018 -0.231 0.863 32.977;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.2 (old=-4.5)
- transform before final EM align:
- 1.057 0.021 0.022 -13.719;
- -0.025 1.044 0.279 -8.820;
- -0.018 -0.231 0.863 32.977;
- 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
- 1.05686 0.02056 0.02170 -13.71878;
- -0.02464 1.04352 0.27875 -8.82042;
- -0.01831 -0.23067 0.86304 32.97652;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.05686 0.02056 0.02170 -13.71878;
- -0.02464 1.04352 0.27875 -8.82042;
- -0.01831 -0.23067 0.86304 32.97652;
- 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) = 3.9 tol 0.000000
- final transform:
- 1.057 0.021 0.022 -13.719;
- -0.025 1.044 0.279 -8.820;
- -0.018 -0.231 0.863 32.977;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 27 minutes and 20 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:11:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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=20.0
- skull bounding box = (57, 30, 25) --> (194, 179, 204)
- using (103, 80, 115) as brain centroid...
- mean wm in atlas = 107, using box (86,62,93) --> (119, 98,137) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 109, scaling input intensities by 0.982
- scaling channel 0 by 0.981651
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.057 0.021 0.022 -13.719;
- -0.025 1.044 0.279 -8.820;
- -0.018 -0.231 0.863 32.977;
- 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 (127, 33, 28) --> (190, 145, 210)
- Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 160.0
- 0 of 71 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (67, 33, 27) --> (129, 136, 211)
- Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 160.0
- 0 of 72 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 118, 60) --> (175, 161, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 160.0
- 0 of 19 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (84, 118, 56) --> (128, 159, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 160.0
- 0 of 10 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (112, 106, 98) --> (143, 172, 131)
- Brain_Stem: limiting intensities to 80.0 --> 160.0
- 0 of 12 (0.0%) samples deleted
- using 184 total control points for intensity normalization...
- bias field = 1.002 +- 0.050
- 0 of 184 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 33, 28) --> (190, 145, 210)
- Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 154.0
- 0 of 116 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (67, 33, 27) --> (129, 136, 211)
- Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 154.0
- 0 of 112 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 118, 60) --> (175, 161, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 154.0
- 0 of 33 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (84, 118, 56) --> (128, 159, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 154.0
- 21 of 44 (47.7%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (112, 106, 98) --> (143, 172, 131)
- Brain_Stem: limiting intensities to 74.0 --> 154.0
- 0 of 74 (0.0%) samples deleted
- using 379 total control points for intensity normalization...
- bias field = 0.990 +- 0.054
- 0 of 358 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 33, 28) --> (190, 145, 210)
- Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 152.0
- 0 of 200 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (67, 33, 27) --> (129, 136, 211)
- Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 152.0
- 0 of 204 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 118, 60) --> (175, 161, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 152.0
- 0 of 40 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (84, 118, 56) --> (128, 159, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 74.0 --> 152.0
- 0 of 42 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (112, 106, 98) --> (143, 172, 131)
- Brain_Stem: limiting intensities to 70.0 --> 152.0
- 0 of 82 (0.0%) samples deleted
- using 568 total control points for intensity normalization...
- bias field = 1.010 +- 0.046
- 1 of 568 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 3 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:13:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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) = 1.02 (predicted orig area = 7.8)
- 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=0.920, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.826 (10.230%), neg=0, invalid=96777
- 0002: dt=129.472000, rms=0.804 (2.702%), neg=0, invalid=96777
- 0003: dt=295.936000, rms=0.789 (1.859%), neg=0, invalid=96777
- 0004: dt=129.472000, rms=0.785 (0.456%), neg=0, invalid=96777
- 0005: dt=295.936000, rms=0.779 (0.775%), neg=0, invalid=96777
- 0006: dt=73.984000, rms=0.777 (0.346%), neg=0, invalid=96777
- 0007: dt=1479.680000, rms=0.765 (1.525%), neg=0, invalid=96777
- 0008: dt=92.480000, rms=0.762 (0.317%), neg=0, invalid=96777
- 0009: dt=443.904000, rms=0.759 (0.363%), neg=0, invalid=96777
- 0010: dt=55.488000, rms=0.758 (0.139%), neg=0, invalid=96777
- 0011: dt=55.488000, rms=0.758 (0.040%), neg=0, invalid=96777
- 0012: dt=55.488000, rms=0.758 (0.051%), neg=0, invalid=96777
- 0013: dt=55.488000, rms=0.757 (0.090%), neg=0, invalid=96777
- 0014: dt=55.488000, rms=0.756 (0.142%), neg=0, invalid=96777
- 0015: dt=55.488000, rms=0.755 (0.155%), neg=0, invalid=96777
- 0016: dt=55.488000, rms=0.754 (0.153%), neg=0, invalid=96777
- 0017: dt=55.488000, rms=0.752 (0.154%), neg=0, invalid=96777
- 0018: dt=55.488000, rms=0.751 (0.154%), neg=0, invalid=96777
- 0019: dt=55.488000, rms=0.750 (0.150%), neg=0, invalid=96777
- 0020: dt=55.488000, rms=0.749 (0.166%), neg=0, invalid=96777
- 0021: dt=55.488000, rms=0.748 (0.167%), neg=0, invalid=96777
- 0022: dt=55.488000, rms=0.747 (0.155%), neg=0, invalid=96777
- 0023: dt=55.488000, rms=0.746 (0.139%), neg=0, invalid=96777
- 0024: dt=55.488000, rms=0.745 (0.126%), neg=0, invalid=96777
- 0025: dt=55.488000, rms=0.744 (0.123%), neg=0, invalid=96777
- 0026: dt=55.488000, rms=0.743 (0.126%), neg=0, invalid=96777
- 0027: dt=55.488000, rms=0.742 (0.149%), neg=0, invalid=96777
- 0028: dt=55.488000, rms=0.741 (0.142%), neg=0, invalid=96777
- 0029: dt=55.488000, rms=0.740 (0.131%), neg=0, invalid=96777
- 0030: dt=55.488000, rms=0.739 (0.113%), neg=0, invalid=96777
- 0031: dt=55.488000, rms=0.738 (0.101%), neg=0, invalid=96777
- 0032: dt=517.888000, rms=0.737 (0.159%), neg=0, invalid=96777
- 0033: dt=27.744000, rms=0.737 (0.001%), neg=0, invalid=96777
- 0034: dt=27.744000, rms=0.737 (0.001%), neg=0, invalid=96777
- 0035: dt=27.744000, rms=0.737 (-0.011%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.737, neg=0, invalid=96777
- 0036: dt=92.480000, rms=0.736 (0.052%), neg=0, invalid=96777
- 0037: dt=369.920000, rms=0.735 (0.237%), neg=0, invalid=96777
- 0038: dt=32.368000, rms=0.735 (0.006%), neg=0, invalid=96777
- 0039: dt=32.368000, rms=0.735 (0.010%), neg=0, invalid=96777
- 0040: dt=32.368000, rms=0.735 (0.002%), neg=0, invalid=96777
- 0041: dt=32.368000, rms=0.735 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.739, neg=0, invalid=96777
- 0042: dt=145.152000, rms=0.722 (2.270%), neg=0, invalid=96777
- 0043: dt=124.416000, rms=0.716 (0.928%), neg=0, invalid=96777
- 0044: dt=36.288000, rms=0.708 (1.005%), neg=0, invalid=96777
- 0045: dt=20.736000, rms=0.707 (0.170%), neg=0, invalid=96777
- 0046: dt=20.736000, rms=0.706 (0.181%), neg=0, invalid=96777
- 0047: dt=20.736000, rms=0.704 (0.308%), neg=0, invalid=96777
- 0048: dt=20.736000, rms=0.701 (0.414%), neg=0, invalid=96777
- 0049: dt=20.736000, rms=0.697 (0.491%), neg=0, invalid=96777
- 0050: dt=20.736000, rms=0.694 (0.558%), neg=0, invalid=96777
- 0051: dt=20.736000, rms=0.689 (0.592%), neg=0, invalid=96777
- 0052: dt=20.736000, rms=0.685 (0.576%), neg=0, invalid=96777
- 0053: dt=20.736000, rms=0.682 (0.555%), neg=0, invalid=96777
- 0054: dt=20.736000, rms=0.678 (0.513%), neg=0, invalid=96777
- 0055: dt=20.736000, rms=0.675 (0.476%), neg=0, invalid=96777
- 0056: dt=20.736000, rms=0.672 (0.425%), neg=0, invalid=96777
- 0057: dt=20.736000, rms=0.670 (0.376%), neg=0, invalid=96777
- 0058: dt=20.736000, rms=0.667 (0.334%), neg=0, invalid=96777
- 0059: dt=20.736000, rms=0.665 (0.280%), neg=0, invalid=96777
- 0060: dt=20.736000, rms=0.664 (0.249%), neg=0, invalid=96777
- 0061: dt=20.736000, rms=0.662 (0.238%), neg=0, invalid=96777
- 0062: dt=20.736000, rms=0.661 (0.236%), neg=0, invalid=96777
- 0063: dt=20.736000, rms=0.659 (0.200%), neg=0, invalid=96777
- 0064: dt=20.736000, rms=0.658 (0.155%), neg=0, invalid=96777
- 0065: dt=20.736000, rms=0.658 (0.110%), neg=0, invalid=96777
- 0066: dt=20.736000, rms=0.657 (0.098%), neg=0, invalid=96777
- 0067: dt=145.152000, rms=0.656 (0.130%), neg=0, invalid=96777
- 0068: dt=6.480000, rms=0.656 (0.000%), neg=0, invalid=96777
- 0069: dt=6.480000, rms=0.656 (0.003%), neg=0, invalid=96777
- 0070: dt=6.480000, rms=0.656 (-0.011%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.656, neg=0, invalid=96777
- 0071: dt=15.552000, rms=0.656 (0.025%), neg=0, invalid=96777
- 0072: dt=20.736000, rms=0.656 (0.019%), neg=0, invalid=96777
- 0073: dt=20.736000, rms=0.656 (0.017%), neg=0, invalid=96777
- 0074: dt=20.736000, rms=0.656 (-0.005%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.681, neg=0, invalid=96777
- 0075: dt=7.157895, rms=0.681 (0.097%), neg=0, invalid=96777
- 0076: dt=2.800000, rms=0.681 (0.015%), neg=0, invalid=96777
- 0077: dt=2.800000, rms=0.681 (0.006%), neg=0, invalid=96777
- 0078: dt=2.800000, rms=0.681 (-0.022%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.681, neg=0, invalid=96777
- 0079: dt=0.000000, rms=0.681 (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=0.747, neg=0, invalid=96777
- 0080: dt=5.676259, rms=0.730 (2.311%), neg=0, invalid=96777
- 0081: dt=2.880000, rms=0.729 (0.101%), neg=0, invalid=96777
- 0082: dt=2.880000, rms=0.729 (-0.020%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.729, neg=0, invalid=96777
- 0083: dt=0.000000, rms=0.729 (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=0.798, neg=0, invalid=96777
- 0084: dt=0.877108, rms=0.795 (0.311%), neg=0, invalid=96777
- 0085: dt=2.204082, rms=0.790 (0.711%), neg=0, invalid=96777
- 0086: dt=1.280000, rms=0.788 (0.144%), neg=0, invalid=96777
- 0087: dt=1.280000, rms=0.787 (0.204%), neg=0, invalid=96777
- 0088: dt=1.280000, rms=0.786 (0.053%), neg=0, invalid=96777
- 0089: dt=1.280000, rms=0.786 (-0.358%), neg=0, invalid=96777
- 0090: dt=0.000000, rms=0.786 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.786, neg=0, invalid=96777
- 0091: dt=0.500000, rms=0.786 (0.058%), neg=0, invalid=96777
- 0092: dt=0.448000, rms=0.786 (0.007%), neg=0, invalid=96777
- 0093: dt=0.448000, rms=0.786 (-0.001%), 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=0.742, neg=0, invalid=96777
- 0094: dt=0.384000, rms=0.723 (2.622%), neg=0, invalid=96777
- 0095: dt=0.000000, rms=0.722 (0.005%), neg=0, invalid=96777
- 0096: dt=0.050000, rms=0.722 (-0.461%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.722, neg=0, invalid=96777
- 0097: dt=0.000000, rms=0.722 (0.000%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.07898 ( 6)
- Left_Lateral_Ventricle (4): linear fit = 0.20 x + 0.0 (2036 voxels, overlap=0.082)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2036 voxels, peak = 5), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.14083 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (1080 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1080 voxels, peak = 7), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.07527 (83)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (426 voxels, overlap=0.049)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (426 voxels, peak = 84), gca=83.5
- gca peak = 0.19192 (97)
- mri peak = 0.12903 (77)
- Left_Pallidum (13): linear fit = 0.79 x + 0.0 (305 voxels, overlap=0.031)
- Left_Pallidum (13): linear fit = 0.79 x + 0.0 (305 voxels, peak = 76), gca=76.1
- gca peak = 0.24007 (63)
- mri peak = 0.06263 (52)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (495 voxels, overlap=0.567)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (495 voxels, peak = 55), gca=55.1
- gca peak = 0.29892 (64)
- mri peak = 0.07822 (59)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (594 voxels, overlap=0.712)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (594 voxels, peak = 58), gca=57.9
- gca peak = 0.12541 (104)
- mri peak = 0.09221 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76693 voxels, overlap=0.760)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76693 voxels, peak = 108), gca=107.6
- gca peak = 0.13686 (104)
- mri peak = 0.08402 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (81954 voxels, overlap=0.713)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (81954 voxels, peak = 109), gca=108.7
- gca peak = 0.11691 (63)
- mri peak = 0.05463 (50)
- Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (23299 voxels, overlap=0.013)
- Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (23299 voxels, peak = 47), gca=46.9
- gca peak = 0.13270 (63)
- mri peak = 0.06566 (52)
- Right_Cerebral_Cortex (42): linear fit = 0.77 x + 0.0 (23129 voxels, overlap=0.030)
- Right_Cerebral_Cortex (42): linear fit = 0.77 x + 0.0 (23129 voxels, peak = 49), gca=48.8
- gca peak = 0.15182 (70)
- mri peak = 0.08707 (61)
- Right_Caudate (50): linear fit = 0.82 x + 0.0 (496 voxels, overlap=0.060)
- Right_Caudate (50): linear fit = 0.82 x + 0.0 (496 voxels, peak = 58), gca=57.8
- gca peak = 0.14251 (76)
- mri peak = 0.07843 (62)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (658 voxels, overlap=0.019)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (658 voxels, peak = 61), gca=61.2
- gca peak = 0.12116 (60)
- mri peak = 0.04924 (52)
- Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (8972 voxels, overlap=0.393)
- Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (8972 voxels, peak = 51), gca=51.3
- gca peak = 0.12723 (61)
- mri peak = 0.03541 (54)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10365 voxels, overlap=0.602)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10365 voxels, peak = 56), gca=55.8
- gca peak = 0.22684 (88)
- mri peak = 0.07428 (89)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7794 voxels, overlap=0.948)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7794 voxels, peak = 90), gca=90.2
- gca peak = 0.21067 (87)
- mri peak = 0.07354 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (7053 voxels, overlap=0.965)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (7053 voxels, peak = 88), gca=88.3
- gca peak = 0.25455 (62)
- mri peak = 0.06376 (61)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (338 voxels, overlap=0.325)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (338 voxels, peak = 57), gca=57.4
- gca peak = 0.39668 (62)
- mri peak = 0.11341 (52)
- Right_Amygdala (54): linear fit = 0.86 x + 0.0 (358 voxels, overlap=0.244)
- Right_Amygdala (54): linear fit = 0.86 x + 0.0 (358 voxels, peak = 53), gca=53.0
- gca peak = 0.10129 (93)
- mri peak = 0.04493 (97)
- Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (6114 voxels, overlap=0.934)
- Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (6114 voxels, peak = 98), gca=98.1
- gca peak = 0.12071 (89)
- mri peak = 0.05059 (91)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4304 voxels, overlap=0.986)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4304 voxels, peak = 91), gca=91.2
- gca peak = 0.13716 (82)
- mri peak = 0.04188 (73)
- Left_Putamen (12): linear fit = 0.92 x + 0.0 (1836 voxels, overlap=0.536)
- Left_Putamen (12): linear fit = 0.92 x + 0.0 (1836 voxels, peak = 75), gca=75.0
- gca peak = 0.15214 (84)
- mri peak = 0.05570 (69)
- Right_Putamen (51): linear fit = 0.83 x + 0.0 (2150 voxels, overlap=0.023)
- Right_Putamen (51): linear fit = 0.83 x + 0.0 (2150 voxels, peak = 70), gca=70.1
- gca peak = 0.08983 (85)
- mri peak = 0.07156 (87)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (11745 voxels, overlap=0.778)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (11745 voxels, peak = 88), gca=88.0
- gca peak = 0.11809 (92)
- mri peak = 0.05832 (89)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (830 voxels, overlap=0.841)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (830 voxels, peak = 96), gca=96.1
- gca peak = 0.12914 (94)
- mri peak = 0.06610 (96)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (887 voxels, overlap=0.860)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (887 voxels, peak = 95), gca=95.4
- gca peak = 0.21100 (36)
- mri peak = 0.50000 (54)
- Third_Ventricle (14): linear fit = 1.49 x + 0.0 (61 voxels, overlap=2.064)
- Third_Ventricle (14): linear fit = 1.49 x + 0.0 (61 voxels, peak = 53), gca=53.5
- gca peak = 0.13542 (27)
- mri peak = 0.12434 (11)
- Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (399 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (399 voxels, peak = 10), gca=9.9
- 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 0.85 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 0.76 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=0.762, neg=0, invalid=96777
- 0098: dt=129.472000, rms=0.758 (0.578%), neg=0, invalid=96777
- 0099: dt=129.472000, rms=0.756 (0.302%), neg=0, invalid=96777
- 0100: dt=129.472000, rms=0.754 (0.225%), neg=0, invalid=96777
- 0101: dt=129.472000, rms=0.753 (0.132%), neg=0, invalid=96777
- 0102: dt=129.472000, rms=0.751 (0.185%), neg=0, invalid=96777
- 0103: dt=73.984000, rms=0.751 (0.046%), neg=0, invalid=96777
- 0104: dt=73.984000, rms=0.750 (0.088%), neg=0, invalid=96777
- 0105: dt=73.984000, rms=0.750 (0.119%), neg=0, invalid=96777
- 0106: dt=73.984000, rms=0.749 (0.130%), neg=0, invalid=96777
- 0107: dt=73.984000, rms=0.748 (0.132%), neg=0, invalid=96777
- 0108: dt=73.984000, rms=0.747 (0.149%), neg=0, invalid=96777
- 0109: dt=73.984000, rms=0.745 (0.142%), neg=0, invalid=96777
- 0110: dt=73.984000, rms=0.745 (0.119%), neg=0, invalid=96777
- 0111: dt=73.984000, rms=0.744 (0.094%), neg=0, invalid=96777
- 0112: dt=73.984000, rms=0.743 (0.092%), neg=0, invalid=96777
- 0113: dt=73.984000, rms=0.742 (0.112%), neg=0, invalid=96777
- 0114: dt=73.984000, rms=0.742 (0.092%), neg=0, invalid=96777
- 0115: dt=73.984000, rms=0.741 (0.084%), neg=0, invalid=96777
- 0116: dt=73.984000, rms=0.740 (0.079%), neg=0, invalid=96777
- 0117: dt=73.984000, rms=0.740 (0.070%), neg=0, invalid=96777
- 0118: dt=73.984000, rms=0.739 (0.078%), neg=0, invalid=96777
- 0119: dt=73.984000, rms=0.739 (0.084%), neg=0, invalid=96777
- 0120: dt=73.984000, rms=0.738 (0.076%), neg=0, invalid=96777
- 0121: dt=73.984000, rms=0.738 (0.077%), neg=0, invalid=96777
- 0122: dt=36.992000, rms=0.738 (0.009%), neg=0, invalid=96777
- 0123: dt=36.992000, rms=0.738 (0.007%), neg=0, invalid=96777
- 0124: dt=0.505750, rms=0.738 (0.000%), neg=0, invalid=96777
- 0125: dt=0.505750, rms=0.738 (0.000%), neg=0, invalid=96777
- 0126: dt=0.252875, rms=0.738 (0.000%), neg=0, invalid=96777
- 0127: dt=0.126438, rms=0.738 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.738, neg=0, invalid=96777
- 0128: dt=0.000000, rms=0.738 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.738, neg=0, invalid=96777
- 0129: dt=0.000000, rms=0.738 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.738, neg=0, invalid=96777
- 0130: dt=0.000000, rms=0.738 (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=0.739, neg=0, invalid=96777
- 0131: dt=75.304540, rms=0.664 (10.116%), neg=0, invalid=96777
- 0132: dt=25.094225, rms=0.647 (2.551%), neg=0, invalid=96777
- 0133: dt=2.800000, rms=0.645 (0.371%), neg=0, invalid=96777
- 0134: dt=8.000000, rms=0.640 (0.722%), neg=0, invalid=96777
- 0135: dt=44.800000, rms=0.628 (1.826%), neg=0, invalid=96777
- 0136: dt=2.800000, rms=0.627 (0.187%), neg=0, invalid=96777
- 0137: dt=8.000000, rms=0.625 (0.339%), neg=0, invalid=96777
- 0138: dt=44.800000, rms=0.619 (1.042%), neg=0, invalid=96777
- 0139: dt=11.200000, rms=0.616 (0.356%), neg=0, invalid=96777
- 0140: dt=13.714286, rms=0.614 (0.336%), neg=0, invalid=96777
- 0141: dt=11.200000, rms=0.613 (0.213%), neg=0, invalid=96777
- 0142: dt=19.200000, rms=0.611 (0.301%), neg=0, invalid=96777
- 0143: dt=8.000000, rms=0.610 (0.229%), neg=0, invalid=96777
- 0144: dt=44.800000, rms=0.608 (0.358%), neg=0, invalid=96777
- 0145: dt=2.800000, rms=0.606 (0.255%), neg=0, invalid=96777
- 0146: dt=7.353535, rms=0.604 (0.294%), neg=0, invalid=96777
- 0147: dt=153.600000, rms=0.600 (0.650%), neg=0, invalid=96777
- 0148: dt=9.486339, rms=0.593 (1.163%), neg=0, invalid=96777
- 0149: dt=11.200000, rms=0.592 (0.300%), neg=0, invalid=96777
- 0150: dt=11.200000, rms=0.591 (0.129%), neg=0, invalid=96777
- 0151: dt=44.800000, rms=0.590 (0.185%), neg=0, invalid=96777
- 0152: dt=8.655738, rms=0.589 (0.166%), neg=0, invalid=96777
- 0153: dt=25.600000, rms=0.588 (0.103%), neg=0, invalid=96777
- 0154: dt=9.600000, rms=0.587 (0.113%), neg=0, invalid=96777
- 0155: dt=19.200000, rms=0.587 (0.077%), neg=0, invalid=96777
- 0156: dt=11.200000, rms=0.586 (0.093%), neg=0, invalid=96777
- 0157: dt=11.200000, rms=0.586 (0.070%), neg=0, invalid=96777
- 0158: dt=11.200000, rms=0.586 (0.068%), neg=0, invalid=96777
- 0159: dt=38.400000, rms=0.585 (0.117%), neg=0, invalid=96777
- 0160: dt=8.380952, rms=0.584 (0.122%), neg=0, invalid=96777
- 0161: dt=25.600000, rms=0.584 (0.089%), neg=0, invalid=96777
- 0162: dt=8.000000, rms=0.583 (0.084%), neg=0, invalid=96777
- 0163: dt=32.000000, rms=0.583 (0.090%), neg=0, invalid=96777
- 0164: dt=8.000000, rms=0.582 (0.095%), neg=0, invalid=96777
- 0165: dt=32.000000, rms=0.582 (0.100%), neg=0, invalid=96777
- 0166: dt=6.400000, rms=0.581 (0.065%), neg=0, invalid=96777
- 0167: dt=153.600000, rms=0.579 (0.438%), neg=0, invalid=96777
- 0168: dt=0.150000, rms=0.579 (0.002%), neg=0, invalid=96777
- 0169: dt=0.004687, rms=0.579 (0.001%), neg=0, invalid=96777
- 0170: dt=0.000586, rms=0.579 (0.000%), neg=0, invalid=96777
- 0171: dt=0.000293, rms=0.579 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.579, neg=0, invalid=96777
- 0172: dt=0.000488, rms=0.579 (0.000%), neg=0, invalid=96777
- 0173: dt=0.000000, rms=0.579 (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=0.601, neg=0, invalid=96777
- 0174: dt=2.305085, rms=0.600 (0.105%), neg=0, invalid=96777
- 0175: dt=0.252000, rms=0.600 (0.015%), neg=0, invalid=96777
- 0176: dt=0.252000, rms=0.600 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.600, neg=0, invalid=96777
- 0177: dt=2.304000, rms=0.600 (0.051%), neg=0, invalid=96777
- 0178: dt=1.008000, rms=0.600 (0.011%), neg=0, invalid=96777
- 0179: dt=1.008000, rms=0.600 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.637, neg=0, invalid=96777
- 0180: dt=1.536313, rms=0.634 (0.516%), neg=0, invalid=96777
- 0181: dt=0.384000, rms=0.634 (0.013%), neg=0, invalid=96777
- 0182: dt=0.384000, rms=0.634 (-0.006%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.634, neg=0, invalid=96777
- 0183: dt=1.536000, rms=0.633 (0.203%), neg=0, invalid=96777
- 0184: dt=0.448000, rms=0.633 (0.015%), neg=0, invalid=96777
- 0185: dt=0.448000, rms=0.633 (-0.001%), 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=0.595, neg=0, invalid=96777
- 0186: dt=0.384000, rms=0.575 (3.369%), neg=0, invalid=96777
- 0187: dt=0.007000, rms=0.574 (0.014%), neg=0, invalid=96777
- 0188: dt=0.007000, rms=0.574 (0.019%), neg=0, invalid=96777
- 0189: dt=0.007000, rms=0.574 (0.036%), neg=0, invalid=96777
- 0190: dt=0.007000, rms=0.574 (0.053%), neg=0, invalid=96777
- 0191: dt=0.007000, rms=0.573 (0.064%), neg=0, invalid=96777
- 0192: dt=0.007000, rms=0.573 (0.075%), neg=0, invalid=96777
- 0193: dt=0.007000, rms=0.573 (0.085%), neg=0, invalid=96777
- 0194: dt=0.007000, rms=0.572 (0.094%), neg=0, invalid=96777
- 0195: dt=0.007000, rms=0.571 (0.099%), neg=0, invalid=96777
- 0196: dt=0.007000, rms=0.571 (0.102%), neg=0, invalid=96777
- 0197: dt=0.007000, rms=0.570 (0.106%), neg=0, invalid=96777
- 0198: dt=0.007000, rms=0.570 (0.107%), neg=0, invalid=96777
- 0199: dt=0.007000, rms=0.569 (0.111%), neg=0, invalid=96777
- 0200: dt=0.007000, rms=0.568 (0.110%), neg=0, invalid=96777
- 0201: dt=0.007000, rms=0.568 (0.108%), neg=0, invalid=96777
- 0202: dt=0.007000, rms=0.567 (0.107%), neg=0, invalid=96777
- 0203: dt=0.007000, rms=0.567 (0.104%), neg=0, invalid=96777
- 0204: dt=0.007000, rms=0.566 (0.101%), neg=0, invalid=96777
- 0205: dt=0.007000, rms=0.565 (0.096%), neg=0, invalid=96777
- 0206: dt=0.007000, rms=0.565 (0.093%), neg=0, invalid=96777
- 0207: dt=0.007000, rms=0.564 (0.090%), neg=0, invalid=96777
- 0208: dt=0.007000, rms=0.564 (0.086%), neg=0, invalid=96777
- 0209: dt=0.007000, rms=0.563 (0.080%), neg=0, invalid=96777
- 0210: dt=0.007000, rms=0.563 (0.078%), neg=0, invalid=96777
- 0211: dt=0.007000, rms=0.563 (0.074%), neg=0, invalid=96777
- 0212: dt=0.007000, rms=0.562 (0.068%), neg=0, invalid=96777
- 0213: dt=0.007000, rms=0.562 (0.063%), neg=0, invalid=96777
- 0214: dt=0.007000, rms=0.562 (0.058%), neg=0, invalid=96777
- 0215: dt=0.007000, rms=0.561 (0.057%), neg=0, invalid=96777
- 0216: dt=0.007000, rms=0.561 (0.053%), neg=0, invalid=96777
- 0217: dt=0.007000, rms=0.561 (0.046%), neg=0, invalid=96777
- 0218: dt=0.007000, rms=0.560 (0.043%), neg=0, invalid=96777
- 0219: dt=0.007000, rms=0.560 (0.041%), neg=0, invalid=96777
- 0220: dt=0.007000, rms=0.560 (0.039%), neg=0, invalid=96777
- 0221: dt=0.007000, rms=0.560 (0.035%), neg=0, invalid=96777
- 0222: dt=0.007000, rms=0.560 (0.035%), neg=0, invalid=96777
- 0223: dt=0.007000, rms=0.559 (0.026%), neg=0, invalid=96777
- 0224: dt=0.007000, rms=0.559 (0.026%), neg=0, invalid=96777
- 0225: dt=0.007000, rms=0.559 (0.027%), neg=0, invalid=96777
- 0226: dt=0.007000, rms=0.559 (0.021%), neg=0, invalid=96777
- 0227: dt=0.007000, rms=0.559 (0.019%), neg=0, invalid=96777
- 0228: dt=0.112000, rms=0.559 (0.011%), neg=0, invalid=96777
- 0229: dt=0.014000, rms=0.559 (0.005%), neg=0, invalid=96777
- 0230: dt=0.014000, rms=0.559 (0.003%), neg=0, invalid=96777
- 0231: dt=0.014000, rms=0.559 (0.005%), neg=0, invalid=96777
- 0232: dt=0.014000, rms=0.559 (0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.559, neg=0, invalid=96777
- 0233: dt=0.112000, rms=0.557 (0.316%), neg=0, invalid=96777
- 0234: dt=0.112000, rms=0.556 (0.244%), neg=0, invalid=96777
- 0235: dt=0.028000, rms=0.555 (0.042%), neg=0, invalid=96777
- 0236: dt=0.028000, rms=0.555 (0.044%), neg=0, invalid=96777
- 0237: dt=0.028000, rms=0.555 (0.080%), neg=0, invalid=96777
- 0238: dt=0.028000, rms=0.554 (0.109%), neg=0, invalid=96777
- 0239: dt=0.028000, rms=0.553 (0.129%), neg=0, invalid=96777
- 0240: dt=0.007000, rms=0.553 (0.004%), neg=0, invalid=96777
- 0241: dt=0.007000, rms=0.553 (0.007%), neg=0, invalid=96777
- 0242: dt=0.007000, rms=0.553 (0.008%), neg=0, invalid=96777
- 0243: dt=0.007000, rms=0.553 (0.015%), neg=0, invalid=96777
- 0244: dt=0.007000, rms=0.553 (0.021%), neg=0, invalid=96777
- 0245: dt=0.007000, rms=0.553 (0.020%), neg=0, invalid=96777
- 0246: dt=0.112000, rms=0.553 (0.075%), neg=0, invalid=96777
- 0247: dt=0.112000, rms=0.552 (0.061%), neg=0, invalid=96777
- 0248: dt=0.007000, rms=0.552 (-0.000%), neg=0, invalid=96777
- 0249: dt=0.007000, rms=0.552 (0.003%), neg=0, invalid=96777
- 0250: dt=0.007000, rms=0.552 (0.006%), neg=0, invalid=96777
- 0251: dt=0.003500, rms=0.552 (0.001%), neg=0, invalid=96777
- 0252: dt=0.003500, rms=0.552 (0.003%), neg=0, invalid=96777
- 0253: dt=0.003500, rms=0.552 (0.004%), neg=0, invalid=96777
- 0254: dt=0.003500, rms=0.552 (0.007%), neg=0, invalid=96777
- 0255: dt=0.003500, rms=0.552 (0.004%), 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=0.550, neg=0, invalid=96777
- 0256: dt=129.472000, rms=0.550 (0.028%), neg=0, invalid=96777
- 0257: dt=73.984000, rms=0.550 (0.007%), neg=0, invalid=96777
- 0258: dt=73.984000, rms=0.550 (0.002%), neg=0, invalid=96777
- 0259: dt=73.984000, rms=0.549 (0.011%), neg=0, invalid=96777
- 0260: dt=73.984000, rms=0.549 (0.007%), neg=0, invalid=96777
- 0261: dt=73.984000, rms=0.549 (0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.549, neg=0, invalid=96777
- 0262: dt=129.472000, rms=0.549 (0.109%), neg=0, invalid=96777
- 0263: dt=129.472000, rms=0.549 (0.046%), neg=0, invalid=96777
- 0264: dt=129.472000, rms=0.548 (0.034%), neg=0, invalid=96777
- 0265: dt=129.472000, rms=0.548 (0.048%), neg=0, invalid=96777
- 0266: dt=129.472000, rms=0.548 (0.034%), neg=0, invalid=96777
- 0267: dt=129.472000, rms=0.548 (0.041%), neg=0, invalid=96777
- 0268: dt=129.472000, rms=0.548 (0.033%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.548, neg=0, invalid=96777
- 0269: dt=36.288000, rms=0.547 (0.166%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0270: dt=82.944000, rms=0.546 (0.143%), neg=0, invalid=96777
- 0271: dt=82.944000, rms=0.545 (0.066%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0272: dt=82.944000, rms=0.546 (-0.534%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.546, neg=0, invalid=96777
- 0273: dt=20.736000, rms=0.544 (0.254%), neg=0, invalid=96777
- 0274: dt=103.680000, rms=0.542 (0.336%), neg=0, invalid=96777
- 0275: dt=15.552000, rms=0.542 (0.142%), neg=0, invalid=96777
- 0276: dt=15.552000, rms=0.541 (0.034%), neg=0, invalid=96777
- 0277: dt=15.552000, rms=0.541 (0.057%), neg=0, invalid=96777
- 0278: dt=15.552000, rms=0.541 (0.072%), neg=0, invalid=96777
- 0279: dt=15.552000, rms=0.540 (0.086%), neg=0, invalid=96777
- 0280: dt=15.552000, rms=0.540 (0.105%), neg=0, invalid=96777
- 0281: dt=15.552000, rms=0.539 (0.100%), neg=0, invalid=96777
- 0282: dt=15.552000, rms=0.539 (0.097%), neg=0, invalid=96777
- 0283: dt=145.152000, rms=0.538 (0.078%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.538, neg=0, invalid=96777
- iter 0, gcam->neg = 21
- after 10 iterations, nbhd size=1, neg = 0
- 0284: dt=44.800000, rms=0.532 (1.138%), neg=0, invalid=96777
- 0285: dt=8.292683, rms=0.530 (0.463%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 13 iterations, nbhd size=2, neg = 0
- 0286: dt=25.600000, rms=0.528 (0.368%), neg=0, invalid=96777
- 0287: dt=6.400000, rms=0.526 (0.327%), neg=0, invalid=96777
- iter 0, gcam->neg = 24
- after 46 iterations, nbhd size=3, neg = 0
- 0288: dt=44.800000, rms=0.523 (0.503%), neg=0, invalid=96777
- 0289: dt=6.774194, rms=0.522 (0.250%), neg=0, invalid=96777
- 0290: dt=6.774194, rms=0.522 (0.105%), neg=0, invalid=96777
- 0291: dt=6.774194, rms=0.521 (0.123%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 37 iterations, nbhd size=4, neg = 0
- 0292: dt=6.774194, rms=0.520 (0.130%), neg=0, invalid=96777
- 0293: dt=6.774194, rms=0.519 (0.206%), neg=0, invalid=96777
- 0294: dt=6.774194, rms=0.518 (0.219%), neg=0, invalid=96777
- 0295: dt=6.774194, rms=0.517 (0.240%), neg=0, invalid=96777
- 0296: dt=6.774194, rms=0.516 (0.229%), neg=0, invalid=96777
- 0297: dt=6.774194, rms=0.514 (0.235%), neg=0, invalid=96777
- 0298: dt=6.774194, rms=0.513 (0.207%), neg=0, invalid=96777
- 0299: dt=6.774194, rms=0.512 (0.192%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 43 iterations, nbhd size=4, neg = 0
- 0300: dt=6.774194, rms=0.512 (0.146%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0301: dt=6.774194, rms=0.511 (0.175%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0302: dt=6.774194, rms=0.510 (0.163%), neg=0, invalid=96777
- 0303: dt=6.774194, rms=0.509 (0.160%), neg=0, invalid=96777
- 0304: dt=6.774194, rms=0.508 (0.147%), neg=0, invalid=96777
- 0305: dt=6.774194, rms=0.508 (0.131%), neg=0, invalid=96777
- 0306: dt=6.774194, rms=0.507 (0.130%), neg=0, invalid=96777
- 0307: dt=6.774194, rms=0.506 (0.113%), neg=0, invalid=96777
- 0308: dt=6.774194, rms=0.506 (0.116%), neg=0, invalid=96777
- 0309: dt=6.774194, rms=0.505 (0.098%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 45 iterations, nbhd size=3, neg = 0
- 0310: dt=44.800000, rms=0.505 (-0.028%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.505, neg=0, invalid=96777
- 0311: dt=44.800000, rms=0.501 (0.785%), neg=0, invalid=96777
- 0312: dt=6.400000, rms=0.501 (0.066%), neg=0, invalid=96777
- 0313: dt=6.400000, rms=0.501 (0.060%), neg=0, invalid=96777
- 0314: dt=6.400000, rms=0.500 (0.091%), neg=0, invalid=96777
- 0315: dt=6.400000, rms=0.500 (0.095%), neg=0, invalid=96777
- 0316: dt=6.400000, rms=0.499 (0.092%), neg=0, invalid=96777
- 0317: dt=6.400000, rms=0.499 (0.090%), neg=0, invalid=96777
- 0318: dt=11.200000, rms=0.499 (0.052%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.506, neg=0, invalid=96777
- iter 0, gcam->neg = 11
- after 21 iterations, nbhd size=2, neg = 0
- 0319: dt=3.456000, rms=0.506 (0.081%), neg=0, invalid=96777
- 0320: dt=0.720000, rms=0.506 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.506, neg=0, invalid=96777
- iter 0, gcam->neg = 12
- after 3 iterations, nbhd size=0, neg = 0
- 0321: dt=1.826087, rms=0.506 (0.050%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 6 iterations, nbhd size=1, neg = 0
- 0322: dt=4.869565, rms=0.505 (0.128%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 5 iterations, nbhd size=1, neg = 0
- 0323: dt=4.032000, rms=0.505 (0.045%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 8 iterations, nbhd size=1, neg = 0
- 0324: dt=4.032000, rms=0.505 (0.031%), neg=0, invalid=96777
- iter 0, gcam->neg = 36
- after 9 iterations, nbhd size=1, neg = 0
- 0325: dt=4.032000, rms=0.505 (-0.033%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.513, neg=0, invalid=96777
- 0326: dt=0.000000, rms=0.513 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.513, neg=0, invalid=96777
- 0327: dt=0.000000, rms=0.513 (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=0.499, neg=0, invalid=96777
- iter 0, gcam->neg = 1004
- after 200 iterations, nbhd size=1, neg = 1
- starting rms=0.006, neg=1, removing folds in lattice....
- iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.006 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0328: dt=2.029326, rms=0.499 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.499, neg=0, invalid=96777
- iter 0, gcam->neg = 1336
- after 43 iterations, nbhd size=1, neg = 0
- 0329: dt=2.183805, rms=0.427 (14.344%), neg=0, invalid=96777
- 0330: dt=0.000016, rms=0.427 (0.005%), neg=0, invalid=96777
- 0331: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777
- 0332: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777
- 0333: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777
- 0334: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777
- 0335: dt=0.000050, rms=0.427 (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=0.399, neg=0, invalid=96777
- 0336: dt=0.000000, rms=0.400 (-0.319%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.400, neg=0, invalid=96777
- 0337: dt=32.368000, rms=0.400 (0.004%), neg=0, invalid=96777
- 0338: dt=8.092000, rms=0.400 (0.000%), neg=0, invalid=96777
- 0339: dt=8.092000, rms=0.400 (0.000%), neg=0, invalid=96777
- 0340: dt=8.092000, rms=0.400 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.401, neg=0, invalid=96777
- 0341: dt=0.000000, rms=0.401 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.401, neg=0, invalid=96777
- 0342: dt=25.920000, rms=0.400 (0.011%), neg=0, invalid=96777
- 0343: dt=9.072000, rms=0.400 (0.001%), neg=0, invalid=96777
- 0344: dt=9.072000, rms=0.400 (0.001%), neg=0, invalid=96777
- 0345: dt=9.072000, rms=0.400 (0.000%), neg=0, invalid=96777
- 0346: dt=9.072000, rms=0.400 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.402, neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 200 iterations, nbhd size=3, neg = 1
- starting rms=0.007, neg=1, removing folds in lattice....
- iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.007 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0347: dt=6.400000, rms=0.402 (0.000%), 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 = 26
- after 200 iterations, nbhd size=3, neg = 2
- starting rms=0.008, neg=2, removing folds in lattice....
- iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.008 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0348: dt=32.000000, rms=0.402 (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=0.406, neg=0, invalid=96777
- iter 0, gcam->neg = 41
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.005, neg=1, removing folds in lattice....
- iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.005 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0349: dt=3.456000, 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
- iter 0, gcam->neg = 35
- after 200 iterations, nbhd size=3, neg = 1
- starting rms=0.004, neg=1, removing folds in lattice....
- iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0350: dt=4.032000, rms=0.406 (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=0.414, neg=0, invalid=96777
- 0351: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.414, neg=0, invalid=96777
- 0352: dt=0.000000, rms=0.414 (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=0.400, neg=0, invalid=96777
- iter 0, gcam->neg = 312
- after 34 iterations, nbhd size=3, neg = 0
- 0353: dt=0.448000, rms=0.391 (2.148%), neg=0, invalid=96777
- 0354: dt=0.000027, rms=0.391 (0.002%), neg=0, invalid=96777
- 0355: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777
- 0356: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777
- 0357: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777
- 0358: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0359: dt=0.005000, rms=0.391 (0.002%), neg=0, invalid=96777
- 0360: dt=0.001250, rms=0.391 (0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.391, neg=0, invalid=96777
- iter 0, gcam->neg = 12
- after 14 iterations, nbhd size=2, neg = 0
- 0361: dt=0.028000, rms=0.391 (0.074%), neg=0, invalid=96777
- 0362: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0363: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0364: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0365: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0366: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0367: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0368: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0369: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0370: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0371: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0372: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0373: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0374: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0375: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0376: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0377: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0378: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0379: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0380: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0381: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0382: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0383: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0384: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0385: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0386: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0387: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0388: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0389: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0390: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0391: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0392: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0393: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- 0394: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 3 hours, 46 minutes and 52 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 16:00:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 16:02:02 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...
- 10449376 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 31 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 16:03:33 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=9.0
- skull bounding box = (43, 0, 0) --> (209, 205, 200)
- using (98, 68, 100) as brain centroid...
- mean wm in atlas = 126, using box (78,43,75) --> (118, 93,124) 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=-4.1, old_max_log_p =-4.2 (thresh=-4.2)
- 1.057 0.021 0.022 -13.719;
- -0.026 1.122 0.300 -18.565;
- -0.018 -0.231 0.863 32.977;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.057 0.021 0.022 -13.719;
- -0.026 1.122 0.300 -18.565;
- -0.018 -0.231 0.863 32.977;
- 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 =-4.1 (thresh=-4.1)
- 1.037 -0.015 0.012 -6.714;
- 0.009 1.080 0.289 -15.944;
- -0.019 -0.235 0.879 31.607;
- 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)
- 1.037 -0.007 -0.017 -4.208;
- 0.009 1.060 0.284 -15.249;
- 0.016 -0.240 0.896 25.836;
- 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=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.041 -0.007 -0.017 -3.726;
- 0.009 1.047 0.312 -16.851;
- 0.015 -0.275 0.887 30.695;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.042 -0.007 -0.017 -3.878;
- 0.009 1.047 0.312 -16.851;
- 0.015 -0.275 0.887 30.695;
- 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
- 1.04224 -0.00684 -0.01683 -3.87823;
- 0.00940 1.04745 0.31168 -16.85081;
- 0.01530 -0.27454 0.88693 30.69490;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.04224 -0.00684 -0.01683 -3.87823;
- 0.00940 1.04745 0.31168 -16.85081;
- 0.01530 -0.27454 0.88693 30.69490;
- 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:
- 1.042 -0.007 -0.017 -3.878;
- 0.009 1.047 0.312 -16.851;
- 0.015 -0.275 0.887 30.695;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.2)
- transform before final EM align:
- 1.042 -0.007 -0.017 -3.878;
- 0.009 1.047 0.312 -16.851;
- 0.015 -0.275 0.887 30.695;
- 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
- 1.04224 -0.00684 -0.01683 -3.87823;
- 0.00940 1.04745 0.31168 -16.85081;
- 0.01530 -0.27454 0.88693 30.69490;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.04224 -0.00684 -0.01683 -3.87823;
- 0.00940 1.04745 0.31168 -16.85081;
- 0.01530 -0.27454 0.88693 30.69490;
- 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: 009: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.042 -0.007 -0.017 -3.878;
- 0.009 1.047 0.312 -16.851;
- 0.015 -0.275 0.887 30.695;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 38 minutes and 18 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 16:41:51 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/sub006/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 = 0.12487 ( 6)
- Left_Lateral_Ventricle (4): linear fit = 0.19 x + 0.0 (899 voxels, overlap=0.007)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (899 voxels, peak = 5), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.13637 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (1122 voxels, overlap=0.008)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1122 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.08549 (89)
- Right_Pallidum (52): linear fit = 0.88 x + 0.0 (505 voxels, overlap=0.058)
- Right_Pallidum (52): linear fit = 0.88 x + 0.0 (505 voxels, peak = 86), gca=85.8
- gca peak = 0.18160 (96)
- mri peak = 0.09195 (85)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (350 voxels, overlap=0.051)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (350 voxels, peak = 84), gca=84.0
- gca peak = 0.27536 (62)
- mri peak = 0.08812 (57)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (595 voxels, overlap=0.440)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (595 voxels, peak = 52), gca=51.8
- gca peak = 0.32745 (63)
- mri peak = 0.08194 (59)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (598 voxels, overlap=0.819)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (598 voxels, peak = 58), gca=58.3
- gca peak = 0.08597 (105)
- mri peak = 0.09455 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45864 voxels, overlap=0.701)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45864 voxels, peak = 107), gca=106.6
- gca peak = 0.09209 (106)
- mri peak = 0.08356 (109)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (47371 voxels, overlap=0.613)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (47371 voxels, peak = 110), gca=109.7
- gca peak = 0.07826 (63)
- mri peak = 0.05887 (52)
- Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (17471 voxels, overlap=0.107)
- Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (17471 voxels, peak = 48), gca=48.2
- gca peak = 0.08598 (64)
- mri peak = 0.07116 (52)
- Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (16663 voxels, overlap=0.067)
- Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (16663 voxels, peak = 48), gca=48.3
- gca peak = 0.24164 (71)
- mri peak = 0.10545 (63)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (826 voxels, overlap=0.190)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (826 voxels, peak = 62), gca=62.1
- gca peak = 0.18227 (75)
- mri peak = 0.08061 (65)
- Left_Caudate (11): linear fit = 0.86 x + 0.0 (1110 voxels, overlap=0.152)
- Left_Caudate (11): linear fit = 0.86 x + 0.0 (1110 voxels, peak = 64), gca=64.1
- gca peak = 0.10629 (62)
- mri peak = 0.05314 (52)
- Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (6613 voxels, overlap=0.861)
- Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (6613 voxels, peak = 54), gca=54.2
- gca peak = 0.11668 (59)
- mri peak = 0.05021 (53)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (6203 voxels, overlap=0.768)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (6203 voxels, peak = 54), gca=54.0
- gca peak = 0.17849 (88)
- mri peak = 0.08202 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6058 voxels, overlap=0.980)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6058 voxels, peak = 89), gca=89.3
- gca peak = 0.16819 (86)
- mri peak = 0.07495 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6015 voxels, overlap=0.984)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6015 voxels, peak = 87), gca=87.3
- gca peak = 0.41688 (64)
- mri peak = 0.08299 (56)
- Left_Amygdala (18): linear fit = 0.86 x + 0.0 (264 voxels, overlap=0.768)
- Left_Amygdala (18): linear fit = 0.86 x + 0.0 (264 voxels, peak = 55), gca=54.7
- gca peak = 0.42394 (62)
- mri peak = 0.10850 (52)
- Right_Amygdala (54): linear fit = 0.86 x + 0.0 (224 voxels, overlap=0.627)
- Right_Amygdala (54): linear fit = 0.86 x + 0.0 (224 voxels, peak = 53), gca=53.0
- gca peak = 0.10041 (96)
- mri peak = 0.05823 (91)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3976 voxels, overlap=0.996)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3976 voxels, peak = 95), gca=94.6
- gca peak = 0.13978 (88)
- mri peak = 0.06134 (90)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, overlap=0.984)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, peak = 88), gca=87.6
- gca peak = 0.08514 (81)
- mri peak = 0.06002 (73)
- Left_Putamen (12): linear fit = 0.87 x + 0.0 (1705 voxels, overlap=0.271)
- Left_Putamen (12): linear fit = 0.87 x + 0.0 (1705 voxels, peak = 70), gca=70.1
- gca peak = 0.09624 (82)
- mri peak = 0.07704 (69)
- Right_Putamen (51): linear fit = 0.85 x + 0.0 (1743 voxels, overlap=0.256)
- Right_Putamen (51): linear fit = 0.85 x + 0.0 (1743 voxels, peak = 69), gca=69.3
- gca peak = 0.07543 (88)
- mri peak = 0.07082 (88)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (12039 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (12039 voxels, peak = 89), gca=89.3
- gca peak = 0.12757 (95)
- mri peak = 0.07129 (89)
- Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1045 voxels, overlap=0.834)
- Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1045 voxels, peak = 94), gca=93.6
- gca peak = 0.17004 (92)
- mri peak = 0.06245 (97)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1262 voxels, overlap=0.899)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1262 voxels, peak = 95), gca=95.2
- gca peak = 0.21361 (36)
- mri peak = 0.07715 (11)
- gca peak = 0.26069 (23)
- mri peak = 0.11330 (12)
- Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (294 voxels, overlap=0.029)
- Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (294 voxels, peak = 8), gca=8.2
- 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 0.83 x + 0.0
- estimating mean wm scale to be 1.02 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 = 0.12487 ( 6)
- Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (899 voxels, overlap=0.781)
- Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (899 voxels, peak = 6), gca=5.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.13637 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1122 voxels, overlap=0.940)
- Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1122 voxels, peak = 7), gca=7.1
- gca peak = 0.27917 (88)
- mri peak = 0.08549 (89)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (505 voxels, overlap=1.022)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (505 voxels, peak = 88), gca=88.0
- gca peak = 0.18877 (84)
- mri peak = 0.09195 (85)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (350 voxels, overlap=1.012)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (350 voxels, peak = 84), gca=83.6
- gca peak = 0.32076 (52)
- mri peak = 0.08812 (57)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (595 voxels, overlap=1.008)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (595 voxels, peak = 52), gca=52.0
- gca peak = 0.30493 (58)
- mri peak = 0.08194 (59)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (598 voxels, overlap=1.003)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (598 voxels, peak = 58), gca=58.0
- gca peak = 0.08542 (107)
- mri peak = 0.09455 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45864 voxels, overlap=0.760)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45864 voxels, peak = 108), gca=107.5
- gca peak = 0.08544 (110)
- mri peak = 0.08356 (109)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47371 voxels, overlap=0.744)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47371 voxels, peak = 110), gca=110.0
- gca peak = 0.09987 (48)
- mri peak = 0.05887 (52)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17471 voxels, overlap=0.995)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17471 voxels, peak = 48), gca=48.0
- gca peak = 0.11781 (48)
- mri peak = 0.07116 (52)
- Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (16663 voxels, overlap=0.995)
- Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (16663 voxels, peak = 50), gca=49.7
- gca peak = 0.24215 (64)
- mri peak = 0.10545 (63)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (826 voxels, overlap=1.006)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (826 voxels, peak = 63), gca=63.0
- gca peak = 0.18458 (64)
- mri peak = 0.08061 (65)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1110 voxels, overlap=1.000)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1110 voxels, peak = 64), gca=64.0
- gca peak = 0.12088 (53)
- mri peak = 0.05314 (52)
- Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (6613 voxels, overlap=0.995)
- Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (6613 voxels, peak = 55), gca=55.4
- gca peak = 0.12940 (55)
- mri peak = 0.05021 (53)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6203 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6203 voxels, peak = 54), gca=54.2
- gca peak = 0.17397 (89)
- mri peak = 0.08202 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6058 voxels, overlap=0.992)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6058 voxels, peak = 89), gca=88.6
- gca peak = 0.16063 (88)
- mri peak = 0.07495 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6015 voxels, overlap=0.997)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6015 voxels, peak = 88), gca=87.6
- gca peak = 0.32010 (55)
- mri peak = 0.08299 (56)
- Left_Amygdala (18): linear fit = 1.07 x + 0.0 (264 voxels, overlap=1.020)
- Left_Amygdala (18): linear fit = 1.07 x + 0.0 (264 voxels, peak = 59), gca=58.6
- gca peak = 0.46062 (53)
- mri peak = 0.10850 (52)
- Right_Amygdala (54): linear fit = 1.07 x + 0.0 (224 voxels, overlap=1.023)
- Right_Amygdala (54): linear fit = 1.07 x + 0.0 (224 voxels, peak = 56), gca=56.4
- gca peak = 0.10422 (93)
- mri peak = 0.05823 (91)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3976 voxels, overlap=0.979)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3976 voxels, peak = 94), gca=94.4
- gca peak = 0.10935 (87)
- mri peak = 0.06134 (90)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, overlap=0.992)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, peak = 87), gca=86.6
- gca peak = 0.09481 (74)
- mri peak = 0.06002 (73)
- Left_Putamen (12): linear fit = 0.98 x + 0.0 (1705 voxels, overlap=1.002)
- Left_Putamen (12): linear fit = 0.98 x + 0.0 (1705 voxels, peak = 72), gca=72.2
- gca peak = 0.12360 (64)
- mri peak = 0.07704 (69)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (1743 voxels, overlap=0.997)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (1743 voxels, peak = 63), gca=63.0
- gca peak = 0.07465 (87)
- mri peak = 0.07082 (88)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (12039 voxels, overlap=0.799)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (12039 voxels, peak = 87), gca=86.6
- gca peak = 0.14053 (93)
- mri peak = 0.07129 (89)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1045 voxels, overlap=0.824)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1045 voxels, peak = 93), gca=92.5
- gca peak = 0.15191 (95)
- mri peak = 0.06245 (97)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1262 voxels, overlap=0.923)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1262 voxels, peak = 95), gca=95.5
- gca peak = 0.35640 (14)
- mri peak = 0.07715 (11)
- gca peak = 0.33827 ( 9)
- mri peak = 0.11330 (12)
- Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (294 voxels, overlap=0.965)
- Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (294 voxels, peak = 9), gca=9.5
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.24950 (33)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.51723 (60)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.62149 (62)
- gca peak Left_choroid_plexus = 0.09108 (48)
- gca peak Right_Inf_Lat_Vent = 0.30433 (27)
- gca peak Right_Accumbens_area = 0.31102 (63)
- gca peak Right_vessel = 0.29571 (59)
- gca peak Right_choroid_plexus = 0.10219 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.14093 (84)
- gca peak non_WM_hypointensities = 0.11402 (54)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.03 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.79 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
- 14369 gm and wm labels changed (%10 to gray, %90 to white out of all changed labels)
- 331 hippocampal voxels changed.
- 12 amygdala voxels changed.
- pass 1: 111271 changed. image ll: -2.298, PF=1.000
- pass 2: 22081 changed. image ll: -2.296, PF=1.000
- pass 3: 9319 changed.
- pass 4: 4519 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 20 minutes and 23 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/cc_up.lta sub006
- 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/sub006/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/norm.mgz
- 16109 voxels in left wm, 22492 in right wm, xrange [125, 130]
- searching rotation angles z=[-8 6], y=[-5 9]
-
searching scale 1 Z rot -7.8
searching scale 1 Z rot -7.6
searching scale 1 Z rot -7.3
searching scale 1 Z rot -7.1
searching scale 1 Z rot -6.8
searching scale 1 Z rot -6.6
searching scale 1 Z rot -6.3
searching scale 1 Z rot -6.1
searching scale 1 Z rot -5.8
searching scale 1 Z rot -5.6
searching scale 1 Z rot -5.3
searching scale 1 Z rot -5.1
searching scale 1 Z rot -4.8
searching scale 1 Z rot -4.6
searching scale 1 Z rot -4.3
searching scale 1 Z rot -4.1
searching scale 1 Z rot -3.8
searching scale 1 Z rot -3.6
searching scale 1 Z rot -3.3
searching scale 1 Z rot -3.1
searching scale 1 Z rot -2.8
searching scale 1 Z rot -2.6
searching scale 1 Z rot -2.3
searching scale 1 Z rot -2.1
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.6
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.1
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.6
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.1
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.4
searching scale 1 Z rot 0.7
searching scale 1 Z rot 0.9
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.4
searching scale 1 Z rot 1.7
searching scale 1 Z rot 1.9
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.4
searching scale 1 Z rot 2.7
searching scale 1 Z rot 2.9
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.4
searching scale 1 Z rot 3.7
searching scale 1 Z rot 3.9
searching scale 1 Z rot 4.2
searching scale 1 Z rot 4.4
searching scale 1 Z rot 4.7
searching scale 1 Z rot 4.9
searching scale 1 Z rot 5.2
searching scale 1 Z rot 5.4
searching scale 1 Z rot 5.7
searching scale 1 Z rot 5.9 global minimum found at slice 127.6, rotations (1.66, -0.84)
- final transformation (x=127.6, yr=1.660, zr=-0.844):
- 0.999 0.015 0.029 -3.518;
- -0.015 1.000 -0.000 47.929;
- -0.029 -0.000 1.000 34.736;
- 0.000 0.000 0.000 1.000;
- updating x range to be [127, 130] in xformed coordinates
- best xformed slice 129
- cc center is found at 129 146 126
- eigenvectors:
- -0.001 -0.004 1.000;
- -0.183 -0.983 -0.004;
- 0.983 -0.183 0.000;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 0.6 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 17:02:53 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 17:02:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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...
- 4588 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 109
- gm peak at 55 (55), valley at 30 (30)
- csf peak at 10, setting threshold to 40
- 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 56 (56), valley at 31 (31)
- csf peak at 10, setting threshold to 40
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 30 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 17:07:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1875800 voxels in mask (pct= 11.18)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 17:07:28 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 (108.0): 107.4 +- 4.6 [80.0 --> 125.0]
- GM (66.0) : 65.4 +- 9.8 [30.0 --> 96.0]
- setting bottom of white matter range to 75.2
- setting top of gray matter range to 85.0
- 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...
- 7560 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 6169 filled
- 374 bright non-wm voxels segmented.
- 4405 diagonally connected voxels added...
- white matter segmentation took 1.9 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...
- 45 voxels added to wm to prevent paths from MTL structures to cortex
- 1381 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 56233 voxels turned on, 47216 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+): 16 found - 16 modified | TOTAL: 16
- pass 2 (xy+): 0 found - 16 modified | TOTAL: 16
- pass 1 (xy-): 20 found - 20 modified | TOTAL: 36
- pass 2 (xy-): 0 found - 20 modified | TOTAL: 36
- pass 1 (yz+): 34 found - 34 modified | TOTAL: 70
- pass 2 (yz+): 0 found - 34 modified | TOTAL: 70
- pass 1 (yz-): 15 found - 15 modified | TOTAL: 85
- pass 2 (yz-): 0 found - 15 modified | TOTAL: 85
- pass 1 (xz+): 24 found - 24 modified | TOTAL: 109
- pass 2 (xz+): 0 found - 24 modified | TOTAL: 109
- pass 1 (xz-): 24 found - 24 modified | TOTAL: 133
- pass 2 (xz-): 0 found - 24 modified | TOTAL: 133
- Iteration Number : 1
- pass 1 (+++): 25 found - 25 modified | TOTAL: 25
- pass 2 (+++): 0 found - 25 modified | TOTAL: 25
- pass 1 (+++): 10 found - 10 modified | TOTAL: 35
- pass 2 (+++): 0 found - 10 modified | TOTAL: 35
- pass 1 (+++): 10 found - 10 modified | TOTAL: 45
- pass 2 (+++): 0 found - 10 modified | TOTAL: 45
- pass 1 (+++): 19 found - 19 modified | TOTAL: 64
- pass 2 (+++): 0 found - 19 modified | TOTAL: 64
- Iteration Number : 1
- pass 1 (++): 213 found - 213 modified | TOTAL: 213
- pass 2 (++): 0 found - 213 modified | TOTAL: 213
- pass 1 (+-): 173 found - 173 modified | TOTAL: 386
- pass 2 (+-): 0 found - 173 modified | TOTAL: 386
- pass 1 (--): 191 found - 191 modified | TOTAL: 577
- pass 2 (--): 0 found - 191 modified | TOTAL: 577
- pass 1 (-+): 190 found - 190 modified | TOTAL: 767
- pass 2 (-+): 0 found - 190 modified | TOTAL: 767
- Iteration Number : 2
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 5 found - 5 modified | TOTAL: 8
- pass 2 (xy-): 0 found - 5 modified | TOTAL: 8
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 9
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 9
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 10
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 10
- pass 1 (xz+): 3 found - 3 modified | TOTAL: 13
- pass 2 (xz+): 0 found - 3 modified | TOTAL: 13
- pass 1 (xz-): 4 found - 4 modified | TOTAL: 17
- pass 2 (xz-): 0 found - 4 modified | TOTAL: 17
- Iteration Number : 2
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 2 found - 2 modified | TOTAL: 4
- pass 2 (+++): 0 found - 2 modified | TOTAL: 4
- pass 1 (+++): 2 found - 2 modified | TOTAL: 6
- pass 2 (+++): 0 found - 2 modified | TOTAL: 6
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 1 found - 1 modified | TOTAL: 2
- pass 2 (-+): 0 found - 1 modified | TOTAL: 2
- Iteration Number : 3
- 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-): 1 found - 1 modified | TOTAL: 3
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 3
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 4
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 4
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 4
- 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 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 4
- 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-): 1 found - 1 modified | TOTAL: 1
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 1
- Iteration Number : 4
- 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 : 4
- 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 : 5
- 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 : 5
- 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 : 5
- 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 = 995 (out of 667295: 0.149109)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 17:10:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 1.057 0.021 0.022 -13.719;
- -0.025 1.044 0.279 -8.820;
- -0.018 -0.231 0.863 32.977;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.057 0.021 0.022 -13.719;
- -0.025 1.044 0.279 -8.820;
- -0.018 -0.231 0.863 32.977;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 914 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75)
- no need to search
- using seed (126, 115, 148), TAL = (2.0, 20.0, 13.0)
- talairach voxel to voxel transform
- 0.945 -0.022 -0.017 13.320;
- 0.016 0.894 -0.289 17.639;
- 0.024 0.238 1.081 -33.213;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (126, 115, 148) --> (2.0, 20.0, 13.0)
- done.
- writing output to filled.mgz...
- filling took 1.0 minutes
- talairach cc position changed to (2.00, 20.00, 13.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, 20.00, 13.00) SRC: (110.41, 79.37, 156.83)
- search lh wm seed point around talairach space (-16.00, 20.00, 13.00), SRC: (144.44, 79.94, 157.71)
- 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 17:11:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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-): 3 found - 3 modified | TOTAL: 5
- pass 2 (xy-): 0 found - 3 modified | TOTAL: 5
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 6
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 6
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 7
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 7
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 8
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 8
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 9
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 9
- 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 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 1 found - 1 modified | TOTAL: 2
- pass 2 (+-): 0 found - 1 modified | TOTAL: 2
- pass 1 (--): 2 found - 2 modified | TOTAL: 4
- pass 2 (--): 0 found - 2 modified | TOTAL: 4
- pass 1 (-+): 0 found - 0 modified | TOTAL: 4
- Iteration Number : 2
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
- 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
- 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 = 14 (out of 319770: 0.004378)
- 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 30: 132 vertices, 158 faces
- slice 40: 5154 vertices, 5422 faces
- slice 50: 15090 vertices, 15484 faces
- slice 60: 27343 vertices, 27780 faces
- slice 70: 40146 vertices, 40596 faces
- slice 80: 52914 vertices, 53297 faces
- slice 90: 65174 vertices, 65598 faces
- slice 100: 78142 vertices, 78578 faces
- slice 110: 90088 vertices, 90497 faces
- slice 120: 102254 vertices, 102675 faces
- slice 130: 113707 vertices, 114156 faces
- slice 140: 125465 vertices, 125866 faces
- slice 150: 135787 vertices, 136156 faces
- slice 160: 145524 vertices, 145859 faces
- slice 170: 154037 vertices, 154323 faces
- slice 180: 161662 vertices, 161914 faces
- slice 190: 167381 vertices, 167600 faces
- slice 200: 171832 vertices, 171986 faces
- slice 210: 172752 vertices, 172782 faces
- slice 220: 172752 vertices, 172782 faces
- slice 230: 172752 vertices, 172782 faces
- slice 240: 172752 vertices, 172782 faces
- slice 250: 172752 vertices, 172782 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...
- 172752 voxel in cpt #1: X=-30 [v=172752,e=518346,f=345564] located at (-26.980938, -19.630371, 40.472919)
- For the whole surface: X=-30 [v=172752,e=518346,f=345564]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 17:11:17 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 17:11:23 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- avg radius = 52.1 mm, total surface area = 91668 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.7 minutes
- Not saving sulc
-
step 000: RMS=0.098 (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=0.036 (target=0.015)
step 025: RMS=0.031 (target=0.015)
step 030: RMS=0.028 (target=0.015)
step 035: RMS=0.025 (target=0.015)
step 040: RMS=0.022 (target=0.015)
step 045: RMS=0.021 (target=0.015)
step 050: RMS=0.020 (target=0.015)
step 055: RMS=0.020 (target=0.015)
step 060: RMS=0.019 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 17:12:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.88 +- 0.55 (0.00-->6.92) (max @ vno 79103 --> 79124)
- face area 0.02 +- 0.03 (-0.34-->0.86)
- scaling brain by 0.280...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.310, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.051, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.496, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.766, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.934, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.044, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.120, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.178, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.235, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.288, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.341, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.397, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.458, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.528, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.603, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.682, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.767, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.856, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.951, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.050, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.154, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.264, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.379, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.499, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.623, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.752, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.886, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.024, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.167, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.315, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.467, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.624, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.785, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.951, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.122, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.296, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.476, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.660, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.848, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.041, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.238, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.439, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.645, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.855, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.069, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.288, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.511, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.738, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.969, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.205, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.445, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.689, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.937, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.190, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.446, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.707, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.971, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.240, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.513, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.790, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.070, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 20881.80
- 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 = 3776.48
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00000
- epoch 3 (K=160.0), pass 1, starting sse = 442.44
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.05/10 = 0.00462
- epoch 4 (K=640.0), pass 1, starting sse = 29.50
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.07/12 = 0.00571
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.10 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 17:18:15 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/sub006/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub006 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=-30 (nv=172752, nf=345564, ne=518346, g=16)
- 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 11 iterations
- marking ambiguous vertices...
- 2478 ambiguous faces found in tessellation
- segmenting defects...
- 25 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 6 into 4
- -merging segment 8 into 7
- -merging segment 11 into 7
- 22 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.9378 (-4.9689)
- -vertex loglikelihood: -6.7130 (-3.3565)
- -normal dot loglikelihood: -3.6670 (-3.6670)
- -quad curv loglikelihood: -6.4196 (-3.2098)
- Total Loglikelihood : -26.7374
- CORRECTING DEFECT 0 (vertices=10, convex hull=18)
- After retessellation of defect 0, euler #=-21 (171201,512909,341687) : difference with theory (-19) = 2
- CORRECTING DEFECT 1 (vertices=90, convex hull=84)
- After retessellation of defect 1, euler #=-20 (171220,513001,341761) : difference with theory (-18) = 2
- CORRECTING DEFECT 2 (vertices=101, convex hull=88)
- After retessellation of defect 2, euler #=-19 (171241,513104,341844) : difference with theory (-17) = 2
- CORRECTING DEFECT 3 (vertices=33, convex hull=70)
- After retessellation of defect 3, euler #=-18 (171262,513194,341914) : difference with theory (-16) = 2
- CORRECTING DEFECT 4 (vertices=228, convex hull=225)
- After retessellation of defect 4, euler #=-16 (171280,513353,342057) : difference with theory (-15) = 1
- CORRECTING DEFECT 5 (vertices=213, convex hull=159)
- After retessellation of defect 5, euler #=-15 (171315,513528,342198) : difference with theory (-14) = 1
- CORRECTING DEFECT 6 (vertices=342, convex hull=236)
- After retessellation of defect 6, euler #=-12 (171346,513753,342395) : difference with theory (-13) = -1
- CORRECTING DEFECT 7 (vertices=6, convex hull=14)
- After retessellation of defect 7, euler #=-11 (171346,513757,342400) : difference with theory (-12) = -1
- CORRECTING DEFECT 8 (vertices=26, convex hull=65)
- After retessellation of defect 8, euler #=-10 (171361,513830,342459) : difference with theory (-11) = -1
- CORRECTING DEFECT 9 (vertices=47, convex hull=45)
- After retessellation of defect 9, euler #=-10 (171374,513891,342507) : difference with theory (-10) = 0
- CORRECTING DEFECT 10 (vertices=25, convex hull=24)
- After retessellation of defect 10, euler #=-9 (171378,513911,342524) : difference with theory (-9) = 0
- CORRECTING DEFECT 11 (vertices=57, convex hull=40)
- After retessellation of defect 11, euler #=-8 (171384,513944,342552) : difference with theory (-8) = 0
- CORRECTING DEFECT 12 (vertices=21, convex hull=32)
- After retessellation of defect 12, euler #=-7 (171388,513967,342572) : difference with theory (-7) = 0
- CORRECTING DEFECT 13 (vertices=12, convex hull=30)
- After retessellation of defect 13, euler #=-6 (171393,513994,342595) : difference with theory (-6) = 0
- CORRECTING DEFECT 14 (vertices=51, convex hull=65)
- After retessellation of defect 14, euler #=-5 (171408,514062,342649) : difference with theory (-5) = 0
- CORRECTING DEFECT 15 (vertices=70, convex hull=61)
- After retessellation of defect 15, euler #=-4 (171415,514107,342688) : difference with theory (-4) = 0
- CORRECTING DEFECT 16 (vertices=23, convex hull=27)
- After retessellation of defect 16, euler #=-3 (171421,514133,342709) : difference with theory (-3) = 0
- CORRECTING DEFECT 17 (vertices=9, convex hull=26)
- After retessellation of defect 17, euler #=-2 (171424,514150,342724) : difference with theory (-2) = 0
- CORRECTING DEFECT 18 (vertices=55, convex hull=68)
- After retessellation of defect 18, euler #=-1 (171437,514214,342776) : difference with theory (-1) = 0
- CORRECTING DEFECT 19 (vertices=34, convex hull=59)
- After retessellation of defect 19, euler #=0 (171445,514261,342816) : difference with theory (0) = 0
- CORRECTING DEFECT 20 (vertices=45, convex hull=95)
- After retessellation of defect 20, euler #=1 (171462,514349,342888) : difference with theory (1) = 0
- CORRECTING DEFECT 21 (vertices=49, convex hull=74)
- After retessellation of defect 21, euler #=2 (171478,514428,342952) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.23 (0.09-->11.19) (max @ vno 73397 --> 77073)
- 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 (0.09-->11.19) (max @ vno 73397 --> 77073)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 81 mutations (34.6%), 153 crossovers (65.4%), 260 vertices were eliminated
- building final representation...
- 1274 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=171478, nf=342952, ne=514428, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 29.8 minutes
- 0 defective edges
- removing intersecting faces
- 000: 202 intersecting
- 001: 2 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 171478 - 514428 + 342952 = 2 --> 0 holes
- F =2V-4: 342952 = 342956-4 (0)
- 2E=3F: 1028856 = 1028856 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 19 intersecting
- 001: 3 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 17:48:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub006 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/sub006/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- 24515 bright wm thresholded.
- 438 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig...
- computing class statistics...
- border white: 318128 voxels (1.90%)
- border gray 352780 voxels (2.10%)
- WM (93.0): 93.8 +- 10.2 [70.0 --> 110.0]
- GM (75.0) : 73.0 +- 13.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.3 (was 70)
- setting MAX_BORDER_WHITE to 116.2 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 29.7 (was 40)
- setting MAX_GRAY to 95.8 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->4.93) (max @ vno 73397 --> 77073)
- face area 0.28 +- 0.12 (0.00-->4.07)
- mean absolute distance = 0.66 +- 0.76
- 4605 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=106, GM=57
- mean inside = 93.4, mean outside = 67.5
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=71.0, 74 (74) missing vertices, mean dist 0.4 [0.5 (%28.2)->0.7 (%71.8))]
- %73 local maxima, %22 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 +- 0.26 (0.11-->7.80) (max @ vno 77073 --> 73397)
- face area 0.28 +- 0.13 (0.00-->6.15)
- mean absolute distance = 0.33 +- 0.46
- 4148 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=10027942.0, rms=14.60
- 001: dt: 0.5000, sse=9368935.0, rms=10.566 (0.000%)
- 002: dt: 0.5000, sse=9359829.0, rms=8.174 (0.000%)
- 003: dt: 0.5000, sse=9455504.0, rms=6.630 (0.000%)
- 004: dt: 0.5000, sse=9669029.0, rms=5.705 (0.000%)
- 005: dt: 0.5000, sse=9780128.0, rms=5.172 (0.000%)
- 006: dt: 0.5000, sse=9891815.0, rms=4.903 (0.000%)
- 007: dt: 0.5000, sse=9901317.0, rms=4.749 (0.000%)
- 008: dt: 0.5000, sse=9908980.0, rms=4.663 (0.000%)
- 009: dt: 0.5000, sse=9865048.0, rms=4.605 (0.000%)
- rms = 4.57, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9860651.0, rms=4.565 (0.000%)
- 011: dt: 0.2500, sse=6112863.0, rms=3.143 (0.000%)
- 012: dt: 0.2500, sse=5634209.5, rms=2.705 (0.000%)
- 013: dt: 0.2500, sse=5322691.0, rms=2.631 (0.000%)
- 014: dt: 0.2500, sse=5252264.5, rms=2.570 (0.000%)
- rms = 2.56, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=5136448.5, rms=2.560 (0.000%)
- 016: dt: 0.1250, sse=4708750.5, rms=2.156 (0.000%)
- 017: dt: 0.1250, sse=4654870.0, rms=2.100 (0.000%)
- rms = 2.09, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=4617372.5, rms=2.093 (0.000%)
- positioning took 2.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 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
- mean border=76.5, 49 (14) missing vertices, mean dist -0.2 [0.4 (%82.0)->0.2 (%18.0))]
- %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 (0.09-->8.01) (max @ vno 77073 --> 73397)
- face area 0.35 +- 0.17 (0.00-->8.31)
- mean absolute distance = 0.21 +- 0.28
- 4675 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6305146.5, rms=7.16
- 019: dt: 0.5000, sse=6108556.5, rms=4.764 (0.000%)
- rms = 4.91, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=5510872.5, rms=3.535 (0.000%)
- 021: dt: 0.2500, sse=5267443.5, rms=2.833 (0.000%)
- 022: dt: 0.2500, sse=5214090.5, rms=2.299 (0.000%)
- 023: dt: 0.2500, sse=5223199.5, rms=2.220 (0.000%)
- 024: dt: 0.2500, sse=5142760.5, rms=2.063 (0.000%)
- rms = 2.09, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.1250, sse=5035590.5, rms=1.913 (0.000%)
- 026: dt: 0.1250, sse=4902379.0, rms=1.694 (0.000%)
- rms = 1.65, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=4851876.0, rms=1.651 (0.000%)
- positioning took 1.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=80.3, 35 (5) missing vertices, mean dist -0.1 [0.2 (%79.1)->0.2 (%20.9))]
- %91 local maxima, % 4 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 (0.10-->8.21) (max @ vno 77073 --> 73397)
- face area 0.34 +- 0.16 (0.00-->8.32)
- mean absolute distance = 0.15 +- 0.22
- 3223 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5480494.5, rms=4.80
- 028: dt: 0.5000, sse=5843610.0, rms=4.653 (0.000%)
- 029: dt: 0.5000, sse=6094991.5, rms=4.548 (0.000%)
- rms = 4.91, time step reduction 1 of 3 to 0.250...
- 030: dt: 0.2500, sse=5307931.5, rms=2.755 (0.000%)
- 031: dt: 0.2500, sse=5336993.5, rms=2.063 (0.000%)
- rms = 2.07, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.1250, sse=5213570.5, rms=1.842 (0.000%)
- 033: dt: 0.1250, sse=5036277.0, rms=1.485 (0.000%)
- 034: dt: 0.1250, sse=4985887.5, rms=1.407 (0.000%)
- rms = 1.41, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4985887.5, rms=1.407 (0.004%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=81.4, 30 (4) missing vertices, mean dist -0.0 [0.2 (%59.5)->0.1 (%40.5))]
- %93 local maxima, % 2 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/sub006/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=5031109.0, rms=1.92
- rms = 3.04, time step reduction 1 of 3 to 0.250...
- 036: dt: 0.2500, sse=5082993.5, rms=1.249 (0.000%)
- 037: dt: 0.2500, sse=5214479.0, rms=1.069 (0.000%)
- rms = 1.06, time step reduction 2 of 3 to 0.125...
- 038: dt: 0.2500, sse=5316066.5, rms=1.065 (0.000%)
- rms = 1.03, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=5339791.5, rms=1.027 (0.000%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- generating cortex label...
- 22 non-cortical segments detected
- only using segment with 2212 vertices
- erasing segment 1 (vno[0] = 73466)
- erasing segment 2 (vno[0] = 78475)
- erasing segment 3 (vno[0] = 100956)
- erasing segment 4 (vno[0] = 112206)
- erasing segment 5 (vno[0] = 122789)
- erasing segment 6 (vno[0] = 123824)
- erasing segment 7 (vno[0] = 123835)
- erasing segment 8 (vno[0] = 123859)
- erasing segment 9 (vno[0] = 124890)
- erasing segment 10 (vno[0] = 127013)
- erasing segment 11 (vno[0] = 127062)
- erasing segment 12 (vno[0] = 127083)
- erasing segment 13 (vno[0] = 128190)
- erasing segment 14 (vno[0] = 129286)
- erasing segment 15 (vno[0] = 131208)
- erasing segment 16 (vno[0] = 131226)
- erasing segment 17 (vno[0] = 132184)
- erasing segment 18 (vno[0] = 133096)
- erasing segment 19 (vno[0] = 133105)
- erasing segment 20 (vno[0] = 133109)
- erasing segment 21 (vno[0] = 134078)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.area
- vertex spacing 0.89 +- 0.25 (0.09-->8.22) (max @ vno 77073 --> 73397)
- face area 0.34 +- 0.16 (0.00-->8.21)
- refinement took 9.4 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 17:57:32 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 17:57:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 52.3 mm, total surface area = 105174 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.113 (target=0.015)
step 005: RMS=0.078 (target=0.015)
step 010: RMS=0.056 (target=0.015)
step 015: RMS=0.045 (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=0.015 (target=0.015)
- inflation complete.
- inflation took 0.6 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
- 242 vertices thresholded to be in k1 ~ [-0.25 0.92], k2 ~ [-0.17 0.07]
- total integrated curvature = 0.488*4pi (6.130) --> 1 handles
- ICI = 1.9, FI = 16.1, variation=257.292
- 156 vertices thresholded to be in [-0.03 0.01]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 128 vertices thresholded to be in [-0.13 0.17]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.026
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 18:00:26 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub006 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 [ sub006/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 [ 311 ]
- Gb_filter = 0
- WARN: S lookup min: -0.410253
- WARN: S explicit min: 0.000000 vertex = 12
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 18:00:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.262...
- 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 %20.43
- pass 1: epoch 2 of 3 starting distance error %20.34
- unfolding complete - removing small folds...
- starting distance error %20.24
- removing remaining folds...
- final distance error %20.25
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.28 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 19:17:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 0.579
- curvature mean = 0.039, std = 0.935
- curvature mean = 0.025, std = 0.829
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 379756.1, tmin=1.3897
- d=32.00 min @ (8.00, 8.00, 0.00) sse = 336884.5, tmin=2.7776
- d=16.00 min @ (0.00, -4.00, -4.00) sse = 296310.6, tmin=4.1916
- d=8.00 min @ (-2.00, 0.00, 0.00) sse = 287756.1, tmin=5.6632
- d=4.00 min @ (0.00, 0.00, 1.00) sse = 286234.4, tmin=7.1875
- d=2.00 min @ (0.50, 1.00, -0.50) sse = 285496.2, tmin=8.7121
- d=1.00 min @ (-0.25, -0.50, 0.25) sse = 285288.4, tmin=10.2292
- d=0.50 min @ (0.00, 0.12, 0.00) sse = 285256.1, tmin=11.7381
- 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 11.74 min
- curvature mean = 0.012, std = 0.938
- curvature mean = 0.014, std = 0.924
- curvature mean = 0.009, std = 0.948
- curvature mean = 0.007, std = 0.963
- curvature mean = 0.006, std = 0.946
- curvature mean = 0.002, std = 0.983
- 2 Reading smoothwm
- curvature mean = -0.022, std = 0.292
- curvature mean = 0.004, std = 0.066
- curvature mean = 0.073, std = 0.308
- curvature mean = 0.004, std = 0.077
- curvature mean = 0.035, std = 0.494
- curvature mean = 0.004, std = 0.083
- curvature mean = 0.020, std = 0.639
- curvature mean = 0.004, std = 0.085
- curvature mean = 0.006, std = 0.758
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 19:53:12 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 19:53:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 19:53:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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...
- 1813 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3786 changed, 171478 examined...
- 001: 799 changed, 15881 examined...
- 002: 222 changed, 4452 examined...
- 003: 84 changed, 1319 examined...
- 004: 34 changed, 498 examined...
- 005: 14 changed, 217 examined...
- 006: 11 changed, 85 examined...
- 007: 2 changed, 46 examined...
- 008: 0 changed, 11 examined...
- 244 labels changed using aseg
- 000: 145 total segments, 102 labels (377 vertices) changed
- 001: 43 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 58 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1900 vertices marked for relabeling...
- 1900 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 18 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 19:54:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub006 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/sub006/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- 24515 bright wm thresholded.
- 438 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig...
- computing class statistics...
- border white: 318128 voxels (1.90%)
- border gray 352780 voxels (2.10%)
- WM (93.0): 93.8 +- 10.2 [70.0 --> 110.0]
- GM (75.0) : 73.0 +- 13.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.3 (was 70)
- setting MAX_BORDER_WHITE to 116.2 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 29.7 (was 40)
- setting MAX_GRAY to 95.8 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=57
- mean inside = 93.4, mean outside = 67.5
- 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/sub006/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->4.93) (max @ vno 73397 --> 77073)
- face area 0.28 +- 0.12 (0.00-->4.07)
- mean absolute distance = 0.66 +- 0.77
- 4633 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 193 points - only 7.25% unknown
- deleting segment 1 with 22 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 6 with 21 points - only 0.00% unknown
- deleting segment 7 with 741 points - only 0.00% unknown
- deleting segment 9 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 10 with 3 points - only 0.00% unknown
- deleting segment 12 with 16 points - only 0.00% unknown
- deleting segment 13 with 13 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- deleting segment 15 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- deleting segment 17 with 8 points - only 0.00% unknown
- mean border=71.0, 74 (74) missing vertices, mean dist 0.4 [0.5 (%28.4)->0.7 (%71.6))]
- %73 local maxima, %22 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 +- 0.26 (0.11-->7.80) (max @ vno 77073 --> 73397)
- face area 0.28 +- 0.13 (0.00-->6.14)
- mean absolute distance = 0.33 +- 0.46
- 4164 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=10060111.0, rms=14.57
- 001: dt: 0.5000, sse=9420631.0, rms=10.543 (0.000%)
- 002: dt: 0.5000, sse=9418131.0, rms=8.156 (0.000%)
- 003: dt: 0.5000, sse=9519878.0, rms=6.618 (0.000%)
- 004: dt: 0.5000, sse=9735789.0, rms=5.693 (0.000%)
- 005: dt: 0.5000, sse=9850333.0, rms=5.165 (0.000%)
- 006: dt: 0.5000, sse=9963383.0, rms=4.895 (0.000%)
- 007: dt: 0.5000, sse=9970060.0, rms=4.742 (0.000%)
- 008: dt: 0.5000, sse=9981884.0, rms=4.655 (0.000%)
- 009: dt: 0.5000, sse=9935452.0, rms=4.600 (0.000%)
- rms = 4.56, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9933331.0, rms=4.559 (0.000%)
- 011: dt: 0.2500, sse=6159862.0, rms=3.139 (0.000%)
- 012: dt: 0.2500, sse=5673852.5, rms=2.701 (0.000%)
- 013: dt: 0.2500, sse=5361696.0, rms=2.628 (0.000%)
- 014: dt: 0.2500, sse=5288730.5, rms=2.568 (0.000%)
- rms = 2.56, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=5172132.5, rms=2.558 (0.000%)
- 016: dt: 0.1250, sse=4745235.5, rms=2.156 (0.000%)
- 017: dt: 0.1250, sse=4692363.0, rms=2.101 (0.000%)
- rms = 2.09, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=4655493.5, rms=2.095 (0.000%)
- positioning took 2.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 244 points - only 8.61% unknown
- deleting segment 1 with 22 points - only 0.00% unknown
- deleting segment 2 with 17 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 19 points - only 0.00% unknown
- deleting segment 7 with 8 points - only 0.00% unknown
- deleting segment 8 with 660 points - only 0.00% unknown
- deleting segment 9 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 15 with 16 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 16 with 1 points - only 0.00% unknown
- deleting segment 17 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 18 with 3 points - only 0.00% unknown
- mean border=76.5, 54 (14) missing vertices, mean dist -0.2 [0.4 (%82.0)->0.2 (%18.0))]
- %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 (0.09-->8.01) (max @ vno 77073 --> 73397)
- face area 0.35 +- 0.17 (0.00-->8.31)
- mean absolute distance = 0.21 +- 0.28
- 4693 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6350666.5, rms=7.15
- 019: dt: 0.5000, sse=6157726.0, rms=4.757 (0.000%)
- rms = 4.90, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=5554555.0, rms=3.530 (0.000%)
- 021: dt: 0.2500, sse=5309827.0, rms=2.830 (0.000%)
- 022: dt: 0.2500, sse=5256700.5, rms=2.297 (0.000%)
- 023: dt: 0.2500, sse=5266794.0, rms=2.219 (0.000%)
- 024: dt: 0.2500, sse=5183961.0, rms=2.063 (0.000%)
- rms = 2.09, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.1250, sse=5076422.5, rms=1.914 (0.000%)
- 026: dt: 0.1250, sse=4942420.0, rms=1.695 (0.000%)
- rms = 1.65, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=4891604.5, rms=1.652 (0.000%)
- positioning took 1.6 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 216 points - only 6.48% unknown
- deleting segment 1 with 21 points - only 0.00% unknown
- deleting segment 2 with 17 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 24 points - only 0.00% unknown
- deleting segment 5 with 700 points - only 0.00% unknown
- deleting segment 6 with 14 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 26 points - only 0.00% unknown
- deleting segment 12 with 18 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 14 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- deleting segment 16 with 6 points - only 0.00% unknown
- mean border=80.2, 36 (5) missing vertices, mean dist -0.1 [0.2 (%79.0)->0.2 (%21.0))]
- %92 local maxima, % 4 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 (0.10-->8.21) (max @ vno 77073 --> 73397)
- face area 0.34 +- 0.16 (0.00-->8.31)
- mean absolute distance = 0.15 +- 0.22
- 3263 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5522440.5, rms=4.79
- 028: dt: 0.5000, sse=5886809.0, rms=4.643 (0.000%)
- 029: dt: 0.5000, sse=6147410.0, rms=4.543 (0.000%)
- rms = 4.91, time step reduction 1 of 3 to 0.250...
- 030: dt: 0.2500, sse=5351452.0, rms=2.754 (0.000%)
- 031: dt: 0.2500, sse=5377083.0, rms=2.060 (0.000%)
- rms = 2.07, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.1250, sse=5253498.0, rms=1.840 (0.000%)
- 033: dt: 0.1250, sse=5076645.5, rms=1.485 (0.000%)
- 034: dt: 0.1250, sse=5025209.0, rms=1.408 (0.000%)
- rms = 1.41, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=5025209.0, rms=1.408 (0.004%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 215 points - only 5.58% unknown
- deleting segment 1 with 21 points - only 0.00% unknown
- deleting segment 2 with 17 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 22 points - only 0.00% unknown
- deleting segment 5 with 707 points - only 0.00% unknown
- deleting segment 6 with 14 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- deleting segment 8 with 35 points - only 0.00% unknown
- deleting segment 9 with 20 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 11 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 7 points - only 0.00% unknown
- mean border=81.3, 31 (4) missing vertices, mean dist -0.0 [0.2 (%59.4)->0.1 (%40.6))]
- %93 local maxima, % 2 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=5070727.0, rms=1.92
- rms = 3.03, time step reduction 1 of 3 to 0.250...
- 036: dt: 0.2500, sse=5124402.0, rms=1.249 (0.000%)
- 037: dt: 0.2500, sse=5259710.5, rms=1.070 (0.000%)
- rms = 1.07, time step reduction 2 of 3 to 0.125...
- 038: dt: 0.2500, sse=5361433.0, rms=1.067 (0.000%)
- rms = 1.03, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=5386527.0, rms=1.029 (0.000%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=46.6, 37 (37) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.3 (%100.0))]
- %14 local maxima, %62 large gradients and %20 min vals, 1854 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=41829020.0, rms=34.18
- 001: dt: 0.5000, sse=29729242.0, rms=28.287 (0.000%)
- 002: dt: 0.5000, sse=21449460.0, rms=23.444 (0.000%)
- 003: dt: 0.5000, sse=15982869.0, rms=19.550 (0.000%)
- 004: dt: 0.5000, sse=12582245.0, rms=16.460 (0.000%)
- 005: dt: 0.5000, sse=10589562.0, rms=14.062 (0.000%)
- 006: dt: 0.5000, sse=9451943.0, rms=12.170 (0.000%)
- 007: dt: 0.5000, sse=8684540.0, rms=10.517 (0.000%)
- 008: dt: 0.5000, sse=8174177.5, rms=9.004 (0.000%)
- 009: dt: 0.5000, sse=7824750.5, rms=7.641 (0.000%)
- 010: dt: 0.5000, sse=7654596.5, rms=6.437 (0.000%)
- 011: dt: 0.5000, sse=7620808.5, rms=5.478 (0.000%)
- 012: dt: 0.5000, sse=7788831.0, rms=4.808 (0.000%)
- 013: dt: 0.5000, sse=7917054.5, rms=4.418 (0.000%)
- 014: dt: 0.5000, sse=8059843.5, rms=4.191 (0.000%)
- 015: dt: 0.5000, sse=8142026.5, rms=4.081 (0.000%)
- 016: dt: 0.5000, sse=8267752.0, rms=3.996 (0.000%)
- rms = 3.95, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.5000, sse=8282918.5, rms=3.953 (0.000%)
- 018: dt: 0.2500, sse=5694765.5, rms=3.099 (0.000%)
- 019: dt: 0.2500, sse=5496246.0, rms=2.870 (0.000%)
- rms = 2.84, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=5338956.0, rms=2.841 (0.000%)
- 021: dt: 0.1250, sse=5070952.5, rms=2.649 (0.000%)
- rms = 2.62, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=5036784.5, rms=2.623 (0.000%)
- positioning took 3.3 minutes
- mean border=43.9, 753 (5) missing vertices, mean dist 0.2 [0.2 (%48.8)->0.6 (%51.2))]
- %33 local maxima, %47 large gradients and %16 min vals, 476 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=5913994.5, rms=5.00
- 023: dt: 0.5000, sse=6323110.0, rms=4.222 (0.000%)
- 024: dt: 0.5000, sse=8048154.5, rms=4.157 (0.000%)
- rms = 4.14, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.5000, sse=8038463.0, rms=4.141 (0.000%)
- 026: dt: 0.2500, sse=6275116.5, rms=3.104 (0.000%)
- 027: dt: 0.2500, sse=6170375.0, rms=2.796 (0.000%)
- rms = 2.79, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=5969225.5, rms=2.793 (0.000%)
- 029: dt: 0.1250, sse=5720778.5, rms=2.553 (0.000%)
- rms = 2.52, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=5693824.5, rms=2.518 (0.000%)
- positioning took 1.2 minutes
- mean border=40.9, 885 (3) missing vertices, mean dist 0.1 [0.2 (%35.5)->0.4 (%64.5))]
- %57 local maxima, %24 large gradients and %15 min vals, 602 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=6194776.0, rms=4.52
- 031: dt: 0.5000, sse=6317909.0, rms=4.116 (0.000%)
- rms = 4.10, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.5000, sse=8341824.5, rms=4.101 (0.000%)
- 033: dt: 0.2500, sse=6203912.5, rms=3.015 (0.000%)
- 034: dt: 0.2500, sse=6381834.5, rms=2.697 (0.000%)
- rms = 2.72, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.1250, sse=6219413.0, rms=2.580 (0.000%)
- 036: dt: 0.1250, sse=5955520.5, rms=2.417 (0.000%)
- rms = 2.39, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=5891363.5, rms=2.393 (0.000%)
- positioning took 1.2 minutes
- mean border=39.4, 1880 (3) missing vertices, mean dist 0.1 [0.2 (%44.4)->0.3 (%55.6))]
- %61 local maxima, %19 large gradients and %15 min vals, 422 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/sub006/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=5991562.0, rms=2.98
- rms = 3.99, time step reduction 1 of 3 to 0.250...
- 038: dt: 0.2500, sse=5783776.5, rms=2.557 (0.000%)
- 039: dt: 0.2500, sse=5942419.5, rms=2.448 (0.000%)
- rms = 2.42, time step reduction 2 of 3 to 0.125...
- 040: dt: 0.2500, sse=6016633.0, rms=2.420 (0.000%)
- 041: dt: 0.1250, sse=5899802.0, rms=2.287 (0.000%)
- rms = 2.27, time step reduction 3 of 3 to 0.062...
- 042: dt: 0.1250, sse=5903649.5, rms=2.271 (0.000%)
- positioning took 0.9 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.area.pial
- vertex spacing 1.01 +- 0.42 (0.07-->8.86) (max @ vno 77073 --> 73397)
- face area 0.41 +- 0.31 (0.00-->9.50)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 171478 vertices processed
- 25000 of 171478 vertices processed
- 50000 of 171478 vertices processed
- 75000 of 171478 vertices processed
- 100000 of 171478 vertices processed
- 125000 of 171478 vertices processed
- 150000 of 171478 vertices processed
- 0 of 171478 vertices processed
- 25000 of 171478 vertices processed
- 50000 of 171478 vertices processed
- 75000 of 171478 vertices processed
- 100000 of 171478 vertices processed
- 125000 of 171478 vertices processed
- 150000 of 171478 vertices processed
- thickness calculation complete, 240:598 truncations.
- 40441 vertices at 0 distance
- 120742 vertices at 1 distance
- 110846 vertices at 2 distance
- 42696 vertices at 3 distance
- 11082 vertices at 4 distance
- 2716 vertices at 5 distance
- 750 vertices at 6 distance
- 254 vertices at 7 distance
- 91 vertices at 8 distance
- 37 vertices at 9 distance
- 23 vertices at 10 distance
- 21 vertices at 11 distance
- 30 vertices at 12 distance
- 16 vertices at 13 distance
- 17 vertices at 14 distance
- 8 vertices at 15 distance
- 11 vertices at 16 distance
- 7 vertices at 17 distance
- 5 vertices at 18 distance
- 3 vertices at 19 distance
- 6 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.thickness
- positioning took 17.8 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 20:12:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 20:12:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- pctsurfcon --s sub006 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts/pctsurfcon.log
- Thu Aug 8 20:12:24 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.wm.mgh --regheader sub006 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 133568
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.wm.mgh
- Dim: 171478 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.gm.mgh --projfrac 0.3 --regheader sub006 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 153059
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.gm.mgh
- Dim: 171478 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.w-g.pct.mgh --annot sub006 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/lh.w-g.pct.mgh --annot sub006 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/lh.w-g.pct.mgh
- Vertex Area is 0.667218 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 2087 1415.694
- 2 1002 caudalanteriorcingulate 1419 970.881
- 3 1003 caudalmiddlefrontal 3985 2657.052
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2537 1656.748
- 6 1006 entorhinal 575 407.499
- 7 1007 fusiform 5408 3712.237
- 8 1008 inferiorparietal 10252 6776.328
- 9 1009 inferiortemporal 6684 4582.200
- 10 1010 isthmuscingulate 2348 1537.153
- 11 1011 lateraloccipital 9326 5996.407
- 12 1012 lateralorbitofrontal 4511 3024.425
- 13 1013 lingual 4757 3296.165
- 14 1014 medialorbitofrontal 3425 2281.483
- 15 1015 middletemporal 5998 4283.024
- 16 1016 parahippocampal 1042 727.525
- 17 1017 paracentral 2679 1757.445
- 18 1018 parsopercularis 3585 2399.116
- 19 1019 parsorbitalis 1202 794.842
- 20 1020 parstriangularis 2543 1678.600
- 21 1021 pericalcarine 2257 1504.341
- 22 1022 postcentral 7698 4989.887
- 23 1023 posteriorcingulate 2513 1640.895
- 24 1024 precentral 8936 5689.858
- 25 1025 precuneus 7701 5090.480
- 26 1026 rostralanteriorcingulate 1900 1246.719
- 27 1027 rostralmiddlefrontal 10703 7305.083
- 28 1028 superiorfrontal 15137 10291.527
- 29 1029 superiorparietal 9869 6443.312
- 30 1030 superiortemporal 6608 4488.436
- 31 1031 supramarginal 8389 5600.073
- 32 1032 frontalpole 380 252.491
- 33 1033 temporalpole 784 570.839
- 34 1034 transversetemporal 845 525.919
- 35 1035 insula 4256 2755.293
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 20:12:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 2087 1416 3779 2.712 0.419 0.119 0.030 17 2.6 bankssts
- 1419 971 3035 3.012 0.581 0.169 0.071 47 4.3 caudalanteriorcingulate
- 3985 2657 7761 2.670 0.495 0.128 0.053 57 7.2 caudalmiddlefrontal
- 2537 1657 3599 2.017 0.441 0.164 0.059 46 6.0 cuneus
- 575 407 2153 3.663 0.827 0.139 0.047 7 1.2 entorhinal
- 5408 3712 12135 2.805 0.544 0.142 0.048 98 11.7 fusiform
- 10252 6776 19259 2.508 0.468 0.131 0.041 141 16.7 inferiorparietal
- 6684 4582 14149 2.623 0.632 0.145 0.057 128 15.2 inferiortemporal
- 2348 1537 4343 2.576 0.845 0.155 0.063 53 5.6 isthmuscingulate
- 9326 5996 15104 2.248 0.461 0.148 0.051 155 19.0 lateraloccipital
- 4511 3024 9097 2.639 0.695 0.157 0.066 105 11.9 lateralorbitofrontal
- 4757 3296 7854 2.170 0.578 0.158 0.071 113 12.2 lingual
- 3425 2281 5652 2.116 0.698 0.146 0.071 96 10.7 medialorbitofrontal
- 5998 4283 14011 2.662 0.629 0.152 0.059 139 13.7 middletemporal
- 1042 728 2600 3.067 0.653 0.124 0.039 12 1.4 parahippocampal
- 2679 1757 5234 2.613 0.525 0.111 0.026 22 3.1 paracentral
- 3585 2399 7228 2.655 0.470 0.134 0.043 53 6.3 parsopercularis
- 1202 795 2720 2.697 0.541 0.169 0.060 27 2.9 parsorbitalis
- 2543 1679 4751 2.486 0.421 0.151 0.054 46 5.6 parstriangularis
- 2257 1504 2742 1.906 0.387 0.132 0.050 28 5.0 pericalcarine
- 7698 4990 12760 2.195 0.549 0.126 0.036 101 11.2 postcentral
- 2513 1641 4838 2.709 0.659 0.164 0.080 58 6.6 posteriorcingulate
- 8936 5690 17489 2.775 0.507 0.112 0.034 98 13.0 precentral
- 7701 5090 14236 2.560 0.508 0.137 0.046 130 13.8 precuneus
- 1900 1247 3957 2.678 0.653 0.157 0.079 62 5.0 rostralanteriorcingulate
- 10703 7305 19791 2.310 0.517 0.163 0.066 256 27.0 rostralmiddlefrontal
- 15137 10292 32166 2.685 0.544 0.136 0.042 221 25.9 superiorfrontal
- 9869 6443 16255 2.281 0.451 0.129 0.038 126 15.1 superiorparietal
- 6608 4488 15508 2.965 0.609 0.122 0.034 71 9.5 superiortemporal
- 8389 5600 16613 2.619 0.501 0.144 0.052 152 17.3 supramarginal
- 380 252 789 2.303 0.566 0.209 0.645 28 18.3 frontalpole
- 784 571 2976 3.741 0.581 0.155 0.060 16 1.8 temporalpole
- 845 526 1597 2.628 0.372 0.138 0.051 11 1.7 transversetemporal
- 4256 2755 8840 3.098 0.688 0.123 0.054 69 10.1 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 20:13:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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...
- 11 labels changed using aseg
- relabeling using gibbs priors...
- 000: 11640 changed, 171478 examined...
- 001: 2841 changed, 44597 examined...
- 002: 855 changed, 14481 examined...
- 003: 375 changed, 4767 examined...
- 004: 212 changed, 2161 examined...
- 005: 96 changed, 1161 examined...
- 006: 38 changed, 522 examined...
- 007: 23 changed, 235 examined...
- 008: 20 changed, 145 examined...
- 009: 11 changed, 106 examined...
- 010: 1 changed, 59 examined...
- 011: 2 changed, 7 examined...
- 012: 2 changed, 12 examined...
- 013: 0 changed, 6 examined...
- 2 labels changed using aseg
- 000: 336 total segments, 257 labels (3762 vertices) changed
- 001: 105 total segments, 26 labels (214 vertices) changed
- 002: 80 total segments, 1 labels (1 vertices) changed
- 003: 79 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 189 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1245 vertices marked for relabeling...
- 1245 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 30 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 20:14:46 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 1737 1169 3047 2.147 0.633 0.169 0.069 40 4.7 G_and_S_frontomargin
- 1889 1237 3422 2.383 0.506 0.146 0.060 37 5.6 G_and_S_occipital_inf
- 1891 1142 3765 2.574 0.539 0.119 0.037 25 3.3 G_and_S_paracentral
- 1824 1243 3729 2.567 0.490 0.150 0.044 29 3.4 G_and_S_subcentral
- 852 595 1658 2.166 0.458 0.230 0.374 63 21.5 G_and_S_transv_frontopol
- 3193 2148 6376 2.589 0.589 0.143 0.063 75 7.5 G_and_S_cingul-Ant
- 2067 1418 4062 2.888 0.460 0.127 0.039 28 3.3 G_and_S_cingul-Mid-Ant
- 1797 1207 3398 2.709 0.515 0.126 0.063 27 3.0 G_and_S_cingul-Mid-Post
- 1115 716 2831 3.195 0.510 0.193 0.085 35 4.2 G_cingul-Post-dorsal
- 480 305 916 2.558 0.883 0.143 0.063 8 1.1 G_cingul-Post-ventral
- 2292 1503 3519 2.015 0.444 0.170 0.065 45 5.7 G_cuneus
- 2154 1428 5200 2.809 0.457 0.149 0.055 42 4.7 G_front_inf-Opercular
- 313 211 656 2.443 0.426 0.171 0.064 7 0.8 G_front_inf-Orbital
- 1592 1049 3519 2.610 0.414 0.162 0.059 37 3.9 G_front_inf-Triangul
- 5422 3699 12513 2.619 0.529 0.175 0.085 157 15.9 G_front_middle
- 10115 6825 23961 2.781 0.557 0.146 0.047 178 19.3 G_front_sup
- 754 461 1743 3.266 0.456 0.125 0.062 10 1.6 G_Ins_lg_and_S_cent_ins
- 991 620 2871 3.622 0.690 0.141 0.061 18 2.3 G_insular_short
- 3173 2021 6460 2.548 0.391 0.157 0.056 67 7.1 G_occipital_middle
- 1833 1159 3279 2.296 0.475 0.142 0.049 26 3.5 G_occipital_sup
- 2350 1511 5812 2.918 0.528 0.149 0.046 51 4.5 G_oc-temp_lat-fusifor
- 3136 2200 5725 2.155 0.589 0.177 0.089 100 9.4 G_oc-temp_med-Lingual
- 1291 889 3727 3.273 0.717 0.126 0.038 14 2.0 G_oc-temp_med-Parahip
- 3051 2056 7614 2.845 0.697 0.179 0.078 84 10.0 G_orbital
- 4175 2737 9599 2.737 0.517 0.144 0.050 75 8.6 G_pariet_inf-Angular
- 4269 2887 9859 2.740 0.498 0.151 0.057 87 10.1 G_pariet_inf-Supramar
- 3559 2334 6755 2.376 0.491 0.142 0.044 58 6.3 G_parietal_sup
- 3211 1999 6003 2.341 0.485 0.135 0.042 53 5.4 G_postcentral
- 3609 2190 8796 3.010 0.455 0.120 0.037 53 6.0 G_precentral
- 3348 2214 7711 2.720 0.504 0.152 0.053 82 6.8 G_precuneus
- 1113 734 2205 2.191 0.714 0.202 0.127 61 6.5 G_rectus
- 499 319 879 2.564 0.933 0.133 0.078 15 1.7 G_subcallosal
- 670 412 1433 2.742 0.366 0.146 0.051 11 1.5 G_temp_sup-G_T_transv
- 2497 1668 7760 3.253 0.579 0.144 0.044 37 4.5 G_temp_sup-Lateral
- 850 595 2382 3.593 0.552 0.113 0.041 6 1.3 G_temp_sup-Plan_polar
- 1029 709 2191 2.672 0.546 0.119 0.043 15 1.3 G_temp_sup-Plan_tempo
- 3537 2418 9164 2.797 0.696 0.173 0.079 103 11.4 G_temporal_inf
- 4024 2921 10745 2.734 0.616 0.174 0.076 123 11.6 G_temporal_middle
- 445 291 651 2.189 0.373 0.138 0.045 6 0.8 Lat_Fis-ant-Horizont
- 417 279 609 2.582 0.396 0.110 0.030 2 0.5 Lat_Fis-ant-Vertical
- 1217 820 1624 2.434 0.379 0.131 0.044 14 2.0 Lat_Fis-post
- 2975 1818 4538 2.099 0.443 0.153 0.059 61 7.2 Pole_occipital
- 2014 1430 6654 3.368 0.775 0.149 0.053 34 4.4 Pole_temporal
- 3300 2189 4297 2.155 0.608 0.128 0.049 37 6.8 S_calcarine
- 3623 2425 4628 2.134 0.652 0.100 0.023 19 3.7 S_central
- 1394 947 1970 2.403 0.452 0.108 0.028 8 1.6 S_cingul-Marginalis
- 736 481 1165 2.690 0.531 0.096 0.026 4 0.8 S_circular_insula_ant
- 1835 1226 3103 2.823 0.582 0.107 0.044 34 4.6 S_circular_insula_inf
- 2151 1456 3355 2.669 0.461 0.113 0.029 14 2.7 S_circular_insula_sup
- 1184 864 2131 2.609 0.442 0.110 0.026 8 1.3 S_collat_transv_ant
- 375 259 522 2.041 0.343 0.146 0.036 4 0.6 S_collat_transv_post
- 2928 1970 4637 2.352 0.440 0.133 0.039 37 4.8 S_front_inf
- 2089 1431 3099 2.169 0.396 0.122 0.037 22 2.9 S_front_middle
- 3628 2471 6259 2.484 0.415 0.115 0.034 38 4.8 S_front_sup
- 500 332 659 2.292 0.414 0.095 0.022 2 0.5 S_interm_prim-Jensen
- 4521 3004 6322 2.184 0.353 0.114 0.030 44 5.7 S_intrapariet_and_P_trans
- 1742 1163 2282 2.165 0.391 0.141 0.043 21 2.9 S_oc_middle_and_Lunatus
- 1724 1116 2290 2.197 0.364 0.123 0.030 16 2.2 S_oc_sup_and_transversal
- 606 421 779 2.107 0.358 0.112 0.024 3 0.7 S_occipital_ant
- 1021 720 1783 2.601 0.428 0.142 0.047 12 1.7 S_oc-temp_lat
- 2070 1466 3358 2.587 0.489 0.122 0.032 17 2.8 S_oc-temp_med_and_Lingual
- 590 389 855 2.173 0.415 0.150 0.051 12 1.1 S_orbital_lateral
- 835 560 1291 2.274 0.784 0.129 0.058 17 1.7 S_orbital_med-olfact
- 1564 1056 2608 2.381 0.579 0.147 0.051 29 2.9 S_orbital-H_Shaped
- 2740 1773 3830 2.311 0.511 0.125 0.038 30 4.5 S_parieto_occipital
- 2101 1369 2887 2.266 0.842 0.162 0.067 61 5.1 S_pericallosal
- 3223 2146 4469 2.279 0.436 0.119 0.033 31 4.2 S_postcentral
- 1958 1312 2909 2.481 0.365 0.104 0.026 13 2.0 S_precentral-inf-part
- 1773 1189 2591 2.489 0.448 0.107 0.026 12 1.8 S_precentral-sup-part
- 1103 736 1564 1.934 0.545 0.132 0.036 14 1.7 S_suborbital
- 1655 1123 2824 2.467 0.449 0.138 0.043 22 2.8 S_subparietal
- 2512 1717 3458 2.254 0.426 0.109 0.025 17 2.7 S_temporal_inf
- 7563 5109 12889 2.542 0.414 0.118 0.034 82 9.9 S_temporal_sup
- 525 349 851 2.728 0.377 0.130 0.034 6 0.8 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 20:15:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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...
- 964 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3465 changed, 171478 examined...
- 001: 815 changed, 14674 examined...
- 002: 221 changed, 4418 examined...
- 003: 70 changed, 1306 examined...
- 004: 38 changed, 425 examined...
- 005: 18 changed, 227 examined...
- 006: 6 changed, 97 examined...
- 007: 2 changed, 32 examined...
- 008: 0 changed, 12 examined...
- 42 labels changed using aseg
- 000: 82 total segments, 49 labels (370 vertices) changed
- 001: 35 total segments, 2 labels (2 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 44 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1232 vertices marked for relabeling...
- 1232 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 18 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 20:16:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 2585 1747 5532 2.995 0.549 0.144 0.052 58 5.7 caudalanteriorcingulate
- 4059 2709 7956 2.674 0.492 0.128 0.053 58 7.3 caudalmiddlefrontal
- 3609 2359 5415 2.123 0.452 0.151 0.051 56 7.4 cuneus
- 575 403 2011 3.578 0.875 0.137 0.045 7 1.1 entorhinal
- 4848 3312 10143 2.752 0.513 0.139 0.046 85 10.2 fusiform
- 9662 6365 18033 2.504 0.470 0.130 0.040 133 15.7 inferiorparietal
- 6594 4535 15065 2.685 0.677 0.150 0.059 135 15.7 inferiortemporal
- 2345 1531 4344 2.588 0.834 0.154 0.063 52 5.6 isthmuscingulate
- 9684 6216 15672 2.248 0.461 0.148 0.052 162 19.8 lateraloccipital
- 4809 3225 9957 2.622 0.741 0.161 0.071 118 13.4 lateralorbitofrontal
- 4776 3307 7882 2.171 0.576 0.158 0.071 113 12.2 lingual
- 2589 1731 4352 2.050 0.695 0.158 0.074 79 8.6 medialorbitofrontal
- 8191 5793 18327 2.668 0.591 0.147 0.054 164 17.2 middletemporal
- 1042 730 2607 3.066 0.657 0.123 0.039 12 1.3 parahippocampal
- 3151 2067 6041 2.584 0.519 0.110 0.028 25 4.0 paracentral
- 3200 2130 6516 2.700 0.441 0.136 0.045 48 5.9 parsopercularis
- 1305 859 2436 2.388 0.499 0.142 0.045 19 2.4 parsorbitalis
- 3386 2238 6226 2.480 0.464 0.151 0.053 61 7.2 parstriangularis
- 2301 1527 2775 1.898 0.392 0.134 0.051 29 5.2 pericalcarine
- 8522 5562 13931 2.198 0.542 0.126 0.035 108 12.2 postcentral
- 2674 1757 5051 2.701 0.663 0.161 0.077 59 6.7 posteriorcingulate
- 8839 5629 17249 2.772 0.514 0.113 0.033 97 12.5 precentral
- 7312 4870 13848 2.573 0.516 0.139 0.047 128 13.3 precuneus
- 2562 1677 4896 2.595 0.653 0.148 0.075 75 6.9 rostralanteriorcingulate
- 7048 4770 13361 2.359 0.526 0.155 0.056 144 15.3 rostralmiddlefrontal
- 16629 11399 34844 2.585 0.556 0.148 0.065 332 51.8 superiorfrontal
- 8053 5220 13213 2.290 0.444 0.128 0.037 103 12.1 superiorparietal
- 9265 6276 21747 2.991 0.647 0.127 0.043 137 17.4 superiortemporal
- 8092 5411 15950 2.613 0.505 0.143 0.051 140 16.7 supramarginal
- 790 493 1526 2.627 0.360 0.140 0.052 11 1.6 transversetemporal
- 3842 2501 8119 3.092 0.635 0.118 0.038 39 5.9 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 20:17:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 3
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 3
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 6
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 6
- 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 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 2 found - 2 modified | TOTAL: 3
- pass 2 (-+): 0 found - 2 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 = 9 (out of 321357: 0.002801)
- 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 30: 847 vertices, 936 faces
- slice 40: 6079 vertices, 6323 faces
- slice 50: 15336 vertices, 15708 faces
- slice 60: 26939 vertices, 27348 faces
- slice 70: 39454 vertices, 39893 faces
- slice 80: 51385 vertices, 51797 faces
- slice 90: 63929 vertices, 64328 faces
- slice 100: 77185 vertices, 77639 faces
- slice 110: 88805 vertices, 89216 faces
- slice 120: 100731 vertices, 101178 faces
- slice 130: 112318 vertices, 112793 faces
- slice 140: 124196 vertices, 124580 faces
- slice 150: 134663 vertices, 135052 faces
- slice 160: 143514 vertices, 143849 faces
- slice 170: 152275 vertices, 152570 faces
- slice 180: 159355 vertices, 159609 faces
- slice 190: 165666 vertices, 165877 faces
- slice 200: 170251 vertices, 170436 faces
- slice 210: 171232 vertices, 171276 faces
- slice 220: 171232 vertices, 171276 faces
- slice 230: 171232 vertices, 171276 faces
- slice 240: 171232 vertices, 171276 faces
- slice 250: 171232 vertices, 171276 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...
- 171232 voxel in cpt #1: X=-44 [v=171232,e=513828,f=342552] located at (28.968430, -19.361048, 41.754677)
- For the whole surface: X=-44 [v=171232,e=513828,f=342552]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 20:17:11 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 20:17:17 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- avg radius = 51.7 mm, total surface area = 91178 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.8 minutes
- Not saving sulc
-
step 000: RMS=0.098 (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=0.023 (target=0.015)
step 050: RMS=0.022 (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 rh Thu Aug 8 20:18:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.88 +- 0.54 (0.00-->6.40) (max @ vno 127943 --> 127944)
- face area 0.02 +- 0.03 (-0.12-->0.57)
- scaling brain by 0.274...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.945, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.683, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.120, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.380, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.537, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.643, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.720, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.780, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.832, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.882, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.932, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.986, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.043, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.105, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.172, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.243, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.320, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.401, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.488, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.580, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.678, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.780, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.888, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.000, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.118, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.240, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.367, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.499, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.636, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.778, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.924, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.075, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.230, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.391, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.555, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.724, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.898, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.077, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.260, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.447, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.639, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.836, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.037, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.243, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.453, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.667, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.887, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.110, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.338, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.570, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.806, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.047, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.292, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.541, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.794, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.052, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.314, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.580, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.850, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.124, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.402, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 20772.79
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00018
- epoch 2 (K=40.0), pass 1, starting sse = 3745.31
- 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 = 451.40
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.06/11 = 0.00515
- epoch 4 (K=640.0), pass 1, starting sse = 32.44
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.10/13 = 0.00754
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.10 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 20:24:21 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/sub006/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub006 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=-44 (nv=171232, nf=342552, ne=513828, g=23)
- 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 11 iterations
- marking ambiguous vertices...
- 3594 ambiguous faces found in tessellation
- segmenting defects...
- 33 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 14 into 11
- 32 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.9592 (-4.9796)
- -vertex loglikelihood: -6.6689 (-3.3344)
- -normal dot loglikelihood: -3.6129 (-3.6129)
- -quad curv loglikelihood: -6.2986 (-3.1493)
- Total Loglikelihood : -26.5396
- CORRECTING DEFECT 0 (vertices=16, convex hull=50)
- After retessellation of defect 0, euler #=-28 (169043,506286,337215) : difference with theory (-29) = -1
- CORRECTING DEFECT 1 (vertices=26, convex hull=56)
- After retessellation of defect 1, euler #=-27 (169052,506335,337256) : difference with theory (-28) = -1
- CORRECTING DEFECT 2 (vertices=15, convex hull=21)
- After retessellation of defect 2, euler #=-26 (169056,506351,337269) : difference with theory (-27) = -1
- CORRECTING DEFECT 3 (vertices=18, convex hull=49)
- After retessellation of defect 3, euler #=-25 (169058,506377,337294) : difference with theory (-26) = -1
- CORRECTING DEFECT 4 (vertices=167, convex hull=117)
- After retessellation of defect 4, euler #=-24 (169095,506537,337418) : difference with theory (-25) = -1
- CORRECTING DEFECT 5 (vertices=52, convex hull=78)
- After retessellation of defect 5, euler #=-23 (169107,506605,337475) : difference with theory (-24) = -1
- CORRECTING DEFECT 6 (vertices=59, convex hull=81)
- After retessellation of defect 6, euler #=-22 (169137,506726,337567) : difference with theory (-23) = -1
- CORRECTING DEFECT 7 (vertices=22, convex hull=30)
- After retessellation of defect 7, euler #=-21 (169140,506744,337583) : difference with theory (-22) = -1
- CORRECTING DEFECT 8 (vertices=34, convex hull=84)
- After retessellation of defect 8, euler #=-20 (169158,506832,337654) : difference with theory (-21) = -1
- CORRECTING DEFECT 9 (vertices=45, convex hull=80)
- After retessellation of defect 9, euler #=-19 (169186,506948,337743) : difference with theory (-20) = -1
- CORRECTING DEFECT 10 (vertices=7, convex hull=22)
- After retessellation of defect 10, euler #=-18 (169189,506961,337754) : difference with theory (-19) = -1
- CORRECTING DEFECT 11 (vertices=190, convex hull=202)
- normal vector of length zero at vertex 169579 with 3 faces
- normal vector of length zero at vertex 169579 with 3 faces
- normal vector of length zero at vertex 169579 with 3 faces
- normal vector of length zero at vertex 169579 with 3 faces
- After retessellation of defect 11, euler #=-16 (169240,507210,337954) : difference with theory (-18) = -2
- CORRECTING DEFECT 12 (vertices=17, convex hull=33)
- After retessellation of defect 12, euler #=-15 (169247,507241,337979) : difference with theory (-17) = -2
- CORRECTING DEFECT 13 (vertices=599, convex hull=272)
- After retessellation of defect 13, euler #=-16 (169424,507944,338504) : difference with theory (-16) = 0
- CORRECTING DEFECT 14 (vertices=5, convex hull=15)
- Warning - incorrect dp selected!!!!(-143.980131 >= -143.980132 )
- After retessellation of defect 14, euler #=-15 (169425,507949,338509) : difference with theory (-15) = 0
- CORRECTING DEFECT 15 (vertices=9, convex hull=18)
- After retessellation of defect 15, euler #=-14 (169428,507960,338518) : difference with theory (-14) = 0
- CORRECTING DEFECT 16 (vertices=11, convex hull=25)
- After retessellation of defect 16, euler #=-13 (169431,507975,338531) : difference with theory (-13) = 0
- CORRECTING DEFECT 17 (vertices=60, convex hull=27)
- Warning - incorrect dp selected!!!!(-76.716434 >= -76.716439 )
- After retessellation of defect 17, euler #=-12 (169436,508000,338552) : difference with theory (-12) = 0
- CORRECTING DEFECT 18 (vertices=17, convex hull=36)
- After retessellation of defect 18, euler #=-11 (169448,508048,338589) : difference with theory (-11) = 0
- CORRECTING DEFECT 19 (vertices=87, convex hull=39)
- After retessellation of defect 19, euler #=-10 (169457,508089,338622) : difference with theory (-10) = 0
- CORRECTING DEFECT 20 (vertices=58, convex hull=50)
- After retessellation of defect 20, euler #=-9 (169466,508136,338661) : difference with theory (-9) = 0
- CORRECTING DEFECT 21 (vertices=29, convex hull=51)
- After retessellation of defect 21, euler #=-8 (169475,508186,338703) : difference with theory (-8) = 0
- CORRECTING DEFECT 22 (vertices=13, convex hull=28)
- After retessellation of defect 22, euler #=-7 (169480,508210,338723) : difference with theory (-7) = 0
- CORRECTING DEFECT 23 (vertices=158, convex hull=52)
- After retessellation of defect 23, euler #=-6 (169491,508263,338766) : difference with theory (-6) = 0
- CORRECTING DEFECT 24 (vertices=20, convex hull=71)
- After retessellation of defect 24, euler #=-5 (169505,508330,338820) : difference with theory (-5) = 0
- CORRECTING DEFECT 25 (vertices=87, convex hull=60)
- After retessellation of defect 25, euler #=-4 (169527,508423,338892) : difference with theory (-4) = 0
- CORRECTING DEFECT 26 (vertices=27, convex hull=26)
- After retessellation of defect 26, euler #=-3 (169530,508440,338907) : difference with theory (-3) = 0
- CORRECTING DEFECT 27 (vertices=91, convex hull=77)
- After retessellation of defect 27, euler #=-2 (169559,508562,339001) : difference with theory (-2) = 0
- CORRECTING DEFECT 28 (vertices=60, convex hull=64)
- After retessellation of defect 28, euler #=-1 (169583,508657,339073) : difference with theory (-1) = 0
- CORRECTING DEFECT 29 (vertices=125, convex hull=102)
- After retessellation of defect 29, euler #=0 (169619,508810,339191) : difference with theory (0) = 0
- CORRECTING DEFECT 30 (vertices=37, convex hull=50)
- After retessellation of defect 30, euler #=1 (169631,508865,339235) : difference with theory (1) = 0
- CORRECTING DEFECT 31 (vertices=27, convex hull=60)
- After retessellation of defect 31, euler #=2 (169645,508929,339286) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.07-->7.64) (max @ vno 43725 --> 169136)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.22 (0.07-->7.64) (max @ vno 43725 --> 169136)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 106 mutations (34.8%), 199 crossovers (65.2%), 88 vertices were eliminated
- building final representation...
- 1587 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=169645, nf=339286, ne=508929, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 22.0 minutes
- 0 defective edges
- removing intersecting faces
- 000: 199 intersecting
- 001: 15 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 169645 - 508929 + 339286 = 2 --> 0 holes
- F =2V-4: 339286 = 339290-4 (0)
- 2E=3F: 1017858 = 1017858 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 30 intersecting
- 001: 2 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 20:46:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub006 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/sub006/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- 25014 bright wm thresholded.
- 438 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig...
- computing class statistics...
- border white: 318128 voxels (1.90%)
- border gray 352780 voxels (2.10%)
- WM (93.0): 93.7 +- 10.3 [70.0 --> 110.0]
- GM (75.0) : 73.1 +- 13.4 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.6 (was 70)
- setting MAX_BORDER_WHITE to 116.3 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.2 (was 40)
- setting MAX_GRAY to 95.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.8 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.02-->5.00) (max @ vno 43725 --> 169070)
- face area 0.28 +- 0.12 (0.00-->2.22)
- mean absolute distance = 0.65 +- 0.73
- 5203 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=106, GM=57
- mean inside = 93.6, mean outside = 67.7
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=71.2, 19 (19) missing vertices, mean dist 0.4 [0.4 (%28.5)->0.7 (%71.5))]
- %74 local maxima, %22 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 (0.07-->4.98) (max @ vno 43725 --> 169070)
- face area 0.28 +- 0.13 (0.00-->1.95)
- mean absolute distance = 0.33 +- 0.46
- 4503 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=9990156.0, rms=14.65
- 001: dt: 0.5000, sse=9387922.0, rms=10.573 (0.000%)
- 002: dt: 0.5000, sse=9285183.0, rms=8.140 (0.000%)
- 003: dt: 0.5000, sse=9331436.0, rms=6.565 (0.000%)
- 004: dt: 0.5000, sse=9548231.0, rms=5.626 (0.000%)
- 005: dt: 0.5000, sse=9633569.0, rms=5.075 (0.000%)
- 006: dt: 0.5000, sse=9750143.0, rms=4.811 (0.000%)
- 007: dt: 0.5000, sse=9731474.0, rms=4.648 (0.000%)
- 008: dt: 0.5000, sse=9764969.0, rms=4.577 (0.000%)
- 009: dt: 0.5000, sse=9673746.0, rms=4.507 (0.000%)
- rms = 4.48, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9707184.0, rms=4.482 (0.000%)
- 011: dt: 0.2500, sse=5934601.0, rms=3.033 (0.000%)
- 012: dt: 0.2500, sse=5435345.0, rms=2.562 (0.000%)
- 013: dt: 0.2500, sse=5103281.0, rms=2.468 (0.000%)
- 014: dt: 0.2500, sse=5028657.0, rms=2.377 (0.000%)
- rms = 2.36, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4909786.0, rms=2.356 (0.000%)
- 016: dt: 0.1250, sse=4550146.5, rms=1.988 (0.000%)
- 017: dt: 0.1250, sse=4497600.0, rms=1.937 (0.000%)
- rms = 1.93, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=4465426.5, rms=1.931 (0.000%)
- positioning took 2.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- mean border=76.9, 33 (1) missing vertices, mean dist -0.3 [0.3 (%83.0)->0.2 (%17.0))]
- %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-->4.65) (max @ vno 43725 --> 169070)
- face area 0.35 +- 0.16 (0.00-->2.52)
- mean absolute distance = 0.20 +- 0.27
- 5040 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6179281.5, rms=7.16
- 019: dt: 0.5000, sse=5953634.5, rms=4.656 (0.000%)
- rms = 4.88, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=5379315.0, rms=3.448 (0.000%)
- 021: dt: 0.2500, sse=5148878.5, rms=2.750 (0.000%)
- 022: dt: 0.2500, sse=5075867.5, rms=2.213 (0.000%)
- 023: dt: 0.2500, sse=5088533.5, rms=2.122 (0.000%)
- 024: dt: 0.2500, sse=5003672.0, rms=1.957 (0.000%)
- rms = 1.98, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.1250, sse=4903640.0, rms=1.819 (0.000%)
- 026: dt: 0.1250, sse=4778593.0, rms=1.615 (0.000%)
- rms = 1.58, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=4730548.0, rms=1.577 (0.000%)
- positioning took 1.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=80.6, 28 (0) missing vertices, mean dist -0.1 [0.2 (%79.0)->0.2 (%21.0))]
- %91 local maxima, % 4 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 (0.08-->4.51) (max @ vno 43725 --> 169070)
- face area 0.34 +- 0.16 (0.00-->2.53)
- mean absolute distance = 0.15 +- 0.21
- 2777 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5347951.5, rms=4.74
- 028: dt: 0.5000, sse=5737506.5, rms=4.523 (0.000%)
- rms = 4.52, time step reduction 1 of 3 to 0.250...
- 029: dt: 0.5000, sse=5971399.0, rms=4.523 (0.000%)
- 030: dt: 0.2500, sse=5333414.5, rms=2.476 (0.000%)
- 031: dt: 0.2500, sse=5356994.5, rms=2.198 (0.000%)
- 032: dt: 0.2500, sse=5267410.5, rms=2.040 (0.000%)
- rms = 2.08, time step reduction 2 of 3 to 0.125...
- 033: dt: 0.1250, sse=5128239.5, rms=1.809 (0.000%)
- 034: dt: 0.1250, sse=4969164.0, rms=1.449 (0.000%)
- 035: dt: 0.1250, sse=4908489.5, rms=1.381 (0.000%)
- rms = 1.39, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=4908489.5, rms=1.381 (0.005%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=81.6, 37 (0) missing vertices, mean dist -0.0 [0.1 (%59.5)->0.1 (%40.5))]
- %93 local maxima, % 2 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/sub006/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4953128.5, rms=1.90
- rms = 3.03, time step reduction 1 of 3 to 0.250...
- 037: dt: 0.2500, sse=5013320.5, rms=1.213 (0.000%)
- 038: dt: 0.2500, sse=5143698.0, rms=1.045 (0.000%)
- rms = 1.04, time step reduction 2 of 3 to 0.125...
- 039: dt: 0.2500, sse=5229137.5, rms=1.042 (0.000%)
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 040: dt: 0.1250, sse=5254944.5, rms=1.006 (0.000%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- generating cortex label...
- 13 non-cortical segments detected
- only using segment with 1951 vertices
- erasing segment 1 (vno[0] = 107042)
- erasing segment 2 (vno[0] = 111864)
- erasing segment 3 (vno[0] = 116863)
- erasing segment 4 (vno[0] = 120328)
- erasing segment 5 (vno[0] = 121221)
- erasing segment 6 (vno[0] = 122277)
- erasing segment 7 (vno[0] = 122408)
- erasing segment 8 (vno[0] = 123167)
- erasing segment 9 (vno[0] = 123288)
- erasing segment 10 (vno[0] = 124218)
- erasing segment 11 (vno[0] = 130353)
- erasing segment 12 (vno[0] = 133485)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.area
- vertex spacing 0.89 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070)
- face area 0.34 +- 0.15 (0.00-->2.54)
- refinement took 9.5 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 20:56:00 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 20:56:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 51.9 mm, total surface area = 104232 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.112 (target=0.015)
step 005: RMS=0.078 (target=0.015)
step 010: RMS=0.055 (target=0.015)
step 015: RMS=0.045 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.031 (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)
- inflation complete.
- inflation took 0.7 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
- 200 vertices thresholded to be in k1 ~ [-0.41 0.19], k2 ~ [-0.13 0.06]
- total integrated curvature = 0.492*4pi (6.177) --> 1 handles
- ICI = 2.0, FI = 17.8, variation=283.367
- 152 vertices thresholded to be in [-0.01 0.01]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 164 vertices thresholded to be in [-0.19 0.10]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.027
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 20:59:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub006 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 [ sub006/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 [ 322 ]
- Gb_filter = 0
- WARN: S lookup min: -0.893362
- WARN: S explicit min: 0.000000 vertex = 407
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 20:59:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.258...
- 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 %20.34
- pass 1: epoch 2 of 3 starting distance error %20.31
- unfolding complete - removing small folds...
- starting distance error %20.25
- removing remaining folds...
- final distance error %20.26
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.19 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 22:10:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 0.581
- curvature mean = 0.025, std = 0.936
- curvature mean = 0.025, std = 0.831
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (0.00, -8.00, 0.00) sse = 349579.9, tmin=3.3531
- d=16.00 min @ (4.00, 4.00, 0.00) sse = 342747.6, tmin=5.0340
- d=8.00 min @ (-2.00, -2.00, 0.00) sse = 331556.2, tmin=6.7395
- d=4.00 min @ (1.00, 0.00, 0.00) sse = 329772.9, tmin=8.4627
- d=2.00 min @ (0.00, 0.00, 0.50) sse = 329564.4, tmin=10.2497
- d=1.00 min @ (0.00, 0.00, -0.25) sse = 329553.1, tmin=11.9913
- d=0.50 min @ (-0.12, 0.00, 0.12) sse = 329507.0, tmin=13.7184
- 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 13.72 min
- curvature mean = 0.010, std = 0.925
- curvature mean = 0.013, std = 0.923
- curvature mean = 0.006, std = 0.928
- curvature mean = 0.006, std = 0.963
- curvature mean = 0.004, std = 0.925
- curvature mean = 0.002, std = 0.983
- 2 Reading smoothwm
- curvature mean = -0.023, std = 0.286
- curvature mean = 0.006, std = 0.068
- curvature mean = 0.070, std = 0.322
- curvature mean = 0.006, std = 0.081
- curvature mean = 0.035, std = 0.514
- curvature mean = 0.006, std = 0.086
- curvature mean = 0.018, std = 0.663
- curvature mean = 0.007, std = 0.089
- curvature mean = 0.006, std = 0.778
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 22:55:50 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 22:55:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 22:56:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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...
- 1364 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3470 changed, 169645 examined...
- 001: 819 changed, 14646 examined...
- 002: 187 changed, 4571 examined...
- 003: 61 changed, 1116 examined...
- 004: 21 changed, 387 examined...
- 005: 5 changed, 124 examined...
- 006: 1 changed, 32 examined...
- 007: 0 changed, 7 examined...
- 218 labels changed using aseg
- 000: 119 total segments, 80 labels (484 vertices) changed
- 001: 43 total segments, 4 labels (5 vertices) changed
- 002: 39 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 50 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1942 vertices marked for relabeling...
- 1942 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 19 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 22:57:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub006 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/sub006/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- 25014 bright wm thresholded.
- 438 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig...
- computing class statistics...
- border white: 318128 voxels (1.90%)
- border gray 352780 voxels (2.10%)
- WM (93.0): 93.7 +- 10.3 [70.0 --> 110.0]
- GM (75.0) : 73.1 +- 13.4 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.6 (was 70)
- setting MAX_BORDER_WHITE to 116.3 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.2 (was 40)
- setting MAX_GRAY to 95.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=57
- mean inside = 93.6, mean outside = 67.7
- 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/sub006/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.02-->5.00) (max @ vno 43725 --> 169070)
- face area 0.28 +- 0.12 (0.00-->2.22)
- mean absolute distance = 0.65 +- 0.73
- 5230 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- deleting segment 5 with 380 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 2 points - only 0.00% unknown
- deleting segment 12 with 8 points - only 0.00% unknown
- mean border=71.2, 19 (19) missing vertices, mean dist 0.4 [0.4 (%28.5)->0.7 (%71.5))]
- %74 local maxima, %22 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 (0.07-->4.98) (max @ vno 43725 --> 169070)
- face area 0.28 +- 0.13 (0.00-->1.95)
- mean absolute distance = 0.33 +- 0.46
- 4530 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=10003488.0, rms=14.64
- 001: dt: 0.5000, sse=9404758.0, rms=10.567 (0.000%)
- 002: dt: 0.5000, sse=9304696.0, rms=8.135 (0.000%)
- 003: dt: 0.5000, sse=9350051.0, rms=6.560 (0.000%)
- 004: dt: 0.5000, sse=9569986.0, rms=5.622 (0.000%)
- 005: dt: 0.5000, sse=9656816.0, rms=5.072 (0.000%)
- 006: dt: 0.5000, sse=9776060.0, rms=4.808 (0.000%)
- 007: dt: 0.5000, sse=9756018.0, rms=4.646 (0.000%)
- 008: dt: 0.5000, sse=9792059.0, rms=4.575 (0.000%)
- 009: dt: 0.5000, sse=9700319.0, rms=4.505 (0.000%)
- rms = 4.48, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9735061.0, rms=4.481 (0.000%)
- 011: dt: 0.2500, sse=5951123.0, rms=3.033 (0.000%)
- 012: dt: 0.2500, sse=5449661.5, rms=2.563 (0.000%)
- 013: dt: 0.2500, sse=5117837.0, rms=2.469 (0.000%)
- 014: dt: 0.2500, sse=5043594.0, rms=2.378 (0.000%)
- rms = 2.36, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4924040.5, rms=2.357 (0.000%)
- 016: dt: 0.1250, sse=4564908.5, rms=1.990 (0.000%)
- 017: dt: 0.1250, sse=4512501.0, rms=1.939 (0.000%)
- rms = 1.93, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=4479939.0, rms=1.934 (0.000%)
- positioning took 3.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 20 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- deleting segment 2 with 255 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 11 points - only 0.00% unknown
- deleting segment 5 with 25 points - only 44.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 19 points - only 0.00% unknown
- deleting segment 8 with 8 points - only 0.00% unknown
- mean border=76.8, 33 (1) missing vertices, mean dist -0.3 [0.3 (%82.9)->0.2 (%17.1))]
- %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-->4.65) (max @ vno 43725 --> 169070)
- face area 0.35 +- 0.16 (0.00-->2.52)
- mean absolute distance = 0.21 +- 0.27
- 5067 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6199635.0, rms=7.16
- 019: dt: 0.5000, sse=5973438.0, rms=4.652 (0.000%)
- rms = 4.88, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=5397965.5, rms=3.445 (0.000%)
- 021: dt: 0.2500, sse=5167652.5, rms=2.749 (0.000%)
- 022: dt: 0.2500, sse=5093224.0, rms=2.213 (0.000%)
- 023: dt: 0.2500, sse=5106467.0, rms=2.123 (0.000%)
- 024: dt: 0.2500, sse=5020157.5, rms=1.958 (0.000%)
- rms = 1.98, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.1250, sse=4920171.0, rms=1.820 (0.000%)
- 026: dt: 0.1250, sse=4796014.0, rms=1.617 (0.000%)
- rms = 1.58, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=4747594.5, rms=1.580 (0.000%)
- positioning took 1.5 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 20 points - only 0.00% unknown
- deleting segment 1 with 10 points - only 0.00% unknown
- deleting segment 2 with 12 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 300 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- deleting segment 6 with 18 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 4 points - only 0.00% unknown
- deleting segment 8 with 31 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 8 points - only 0.00% unknown
- mean border=80.5, 27 (0) missing vertices, mean dist -0.1 [0.2 (%78.9)->0.2 (%21.1))]
- %92 local maxima, % 4 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 (0.06-->4.57) (max @ vno 43725 --> 169070)
- face area 0.34 +- 0.16 (0.00-->2.52)
- mean absolute distance = 0.15 +- 0.21
- 2870 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5364998.0, rms=4.74
- 028: dt: 0.5000, sse=5754745.0, rms=4.519 (0.000%)
- rms = 4.52, time step reduction 1 of 3 to 0.250...
- 029: dt: 0.2500, sse=5142845.0, rms=2.842 (0.000%)
- 030: dt: 0.2500, sse=4988408.0, rms=2.323 (0.000%)
- 031: dt: 0.2500, sse=5072433.0, rms=1.909 (0.000%)
- rms = 1.99, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.1250, sse=4977359.5, rms=1.707 (0.000%)
- 033: dt: 0.1250, sse=4858171.0, rms=1.407 (0.000%)
- 034: dt: 0.1250, sse=4822910.0, rms=1.357 (0.000%)
- rms = 1.37, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4822910.0, rms=1.357 (0.010%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 20 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- deleting segment 2 with 16 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- deleting segment 4 with 12 points - only 0.00% unknown
- deleting segment 5 with 280 points - only 0.00% unknown
- deleting segment 6 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- deleting segment 9 with 18 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- deleting segment 11 with 30 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 12 points - only 0.00% unknown
- mean border=81.6, 31 (0) missing vertices, mean dist -0.0 [0.1 (%59.4)->0.1 (%40.6))]
- %93 local maxima, % 2 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=4869947.5, rms=1.89
- rms = 2.97, time step reduction 1 of 3 to 0.250...
- 036: dt: 0.2500, sse=4939095.5, rms=1.211 (0.000%)
- 037: dt: 0.2500, sse=5076491.0, rms=1.035 (0.000%)
- rms = 1.04, time step reduction 2 of 3 to 0.125...
- rms = 1.02, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=5079325.0, rms=1.016 (0.000%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- smoothing surface for 5 iterations...
- mean border=46.6, 53 (53) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.3 (%100.0))]
- %14 local maxima, %62 large gradients and %20 min vals, 1777 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=42034216.0, rms=34.46
- 001: dt: 0.5000, sse=29884576.0, rms=28.534 (0.000%)
- 002: dt: 0.5000, sse=21492024.0, rms=23.613 (0.000%)
- 003: dt: 0.5000, sse=15902650.0, rms=19.644 (0.000%)
- 004: dt: 0.5000, sse=12446432.0, rms=16.501 (0.000%)
- 005: dt: 0.5000, sse=10397814.0, rms=14.072 (0.000%)
- 006: dt: 0.5000, sse=9310842.0, rms=12.188 (0.000%)
- 007: dt: 0.5000, sse=8615309.0, rms=10.572 (0.000%)
- 008: dt: 0.5000, sse=8150395.5, rms=9.098 (0.000%)
- 009: dt: 0.5000, sse=7844656.5, rms=7.741 (0.000%)
- 010: dt: 0.5000, sse=7717932.0, rms=6.564 (0.000%)
- 011: dt: 0.5000, sse=7694301.5, rms=5.626 (0.000%)
- 012: dt: 0.5000, sse=7799948.5, rms=4.951 (0.000%)
- 013: dt: 0.5000, sse=7930760.0, rms=4.514 (0.000%)
- 014: dt: 0.5000, sse=8099019.5, rms=4.289 (0.000%)
- 015: dt: 0.5000, sse=8210826.0, rms=4.154 (0.000%)
- 016: dt: 0.5000, sse=8267964.5, rms=4.070 (0.000%)
- rms = 4.02, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.5000, sse=8310543.5, rms=4.022 (0.000%)
- 018: dt: 0.2500, sse=5667292.0, rms=3.160 (0.000%)
- 019: dt: 0.2500, sse=5442487.5, rms=2.929 (0.000%)
- rms = 2.90, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=5284241.5, rms=2.899 (0.000%)
- 021: dt: 0.1250, sse=5025618.5, rms=2.716 (0.000%)
- rms = 2.69, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=4989413.5, rms=2.691 (0.000%)
- positioning took 3.2 minutes
- mean border=44.0, 754 (9) missing vertices, mean dist 0.2 [0.2 (%48.6)->0.5 (%51.4))]
- %34 local maxima, %46 large gradients and %16 min vals, 421 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=5811038.0, rms=4.88
- 023: dt: 0.5000, sse=6232976.0, rms=4.133 (0.000%)
- rms = 4.11, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.5000, sse=7965109.0, rms=4.112 (0.000%)
- 025: dt: 0.2500, sse=6002721.5, rms=3.127 (0.000%)
- 026: dt: 0.2500, sse=6037564.5, rms=2.869 (0.000%)
- rms = 2.85, time step reduction 2 of 3 to 0.125...
- 027: dt: 0.2500, sse=5879275.5, rms=2.848 (0.000%)
- 028: dt: 0.1250, sse=5651194.0, rms=2.628 (0.000%)
- rms = 2.59, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=5624315.5, rms=2.588 (0.000%)
- positioning took 1.0 minutes
- mean border=41.2, 917 (8) missing vertices, mean dist 0.1 [0.2 (%36.6)->0.4 (%63.4))]
- %57 local maxima, %23 large gradients and %16 min vals, 581 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=6056351.0, rms=4.36
- 030: dt: 0.5000, sse=6282195.0, rms=4.138 (0.000%)
- rms = 4.13, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.5000, sse=8222272.0, rms=4.128 (0.000%)
- 032: dt: 0.2500, sse=6136946.0, rms=3.043 (0.000%)
- 033: dt: 0.2500, sse=6323475.5, rms=2.712 (0.000%)
- rms = 2.74, time step reduction 2 of 3 to 0.125...
- 034: dt: 0.1250, sse=6165397.5, rms=2.598 (0.000%)
- 035: dt: 0.1250, sse=5898154.0, rms=2.439 (0.000%)
- rms = 2.41, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=5838201.0, rms=2.414 (0.000%)
- positioning took 1.1 minutes
- mean border=39.9, 1803 (5) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.3 (%54.9))]
- %61 local maxima, %18 large gradients and %16 min vals, 419 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/sub006/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=5926427.0, rms=2.93
- rms = 3.94, time step reduction 1 of 3 to 0.250...
- 037: dt: 0.2500, sse=5730611.5, rms=2.536 (0.000%)
- 038: dt: 0.2500, sse=5896865.0, rms=2.457 (0.000%)
- rms = 2.44, time step reduction 2 of 3 to 0.125...
- 039: dt: 0.2500, sse=5980395.5, rms=2.440 (0.000%)
- 040: dt: 0.1250, sse=5854210.5, rms=2.301 (0.000%)
- rms = 2.28, time step reduction 3 of 3 to 0.062...
- 041: dt: 0.1250, sse=5855223.5, rms=2.279 (0.000%)
- positioning took 0.9 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.area.pial
- vertex spacing 1.01 +- 0.42 (0.05-->8.48) (max @ vno 120578 --> 119429)
- face area 0.41 +- 0.30 (0.00-->9.41)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 169645 vertices processed
- 25000 of 169645 vertices processed
- 50000 of 169645 vertices processed
- 75000 of 169645 vertices processed
- 100000 of 169645 vertices processed
- 125000 of 169645 vertices processed
- 150000 of 169645 vertices processed
- 0 of 169645 vertices processed
- 25000 of 169645 vertices processed
- 50000 of 169645 vertices processed
- 75000 of 169645 vertices processed
- 100000 of 169645 vertices processed
- 125000 of 169645 vertices processed
- 150000 of 169645 vertices processed
- thickness calculation complete, 164:643 truncations.
- 40505 vertices at 0 distance
- 121379 vertices at 1 distance
- 109370 vertices at 2 distance
- 40989 vertices at 3 distance
- 10693 vertices at 4 distance
- 2358 vertices at 5 distance
- 619 vertices at 6 distance
- 204 vertices at 7 distance
- 91 vertices at 8 distance
- 51 vertices at 9 distance
- 32 vertices at 10 distance
- 31 vertices at 11 distance
- 28 vertices at 12 distance
- 16 vertices at 13 distance
- 8 vertices at 14 distance
- 7 vertices at 15 distance
- 8 vertices at 16 distance
- 9 vertices at 17 distance
- 9 vertices at 18 distance
- 3 vertices at 19 distance
- 8 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.thickness
- positioning took 18.1 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 23:15:26 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 23:15:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- pctsurfcon --s sub006 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts/pctsurfcon.log
- Thu Aug 8 23:15:31 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.wm.mgh --regheader sub006 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 132232
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.wm.mgh
- Dim: 169645 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.gm.mgh --projfrac 0.3 --regheader sub006 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 151597
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.gm.mgh
- Dim: 169645 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.w-g.pct.mgh --annot sub006 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.w-g.pct.mgh --annot sub006 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.w-g.pct.mgh
- Vertex Area is 0.667852 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1610 1110.019
- 2 2002 caudalanteriorcingulate 1502 1063.116
- 3 2003 caudalmiddlefrontal 3799 2611.014
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2768 1817.631
- 6 2006 entorhinal 486 368.606
- 7 2007 fusiform 6320 4272.622
- 8 2008 inferiorparietal 11478 7683.567
- 9 2009 inferiortemporal 5811 3928.208
- 10 2010 isthmuscingulate 1736 1132.247
- 11 2011 lateraloccipital 9606 6132.968
- 12 2012 lateralorbitofrontal 4897 3264.001
- 13 2013 lingual 4996 3427.336
- 14 2014 medialorbitofrontal 2949 1973.371
- 15 2015 middletemporal 5856 4037.792
- 16 2016 parahippocampal 1110 765.764
- 17 2017 paracentral 3361 2175.972
- 18 2018 parsopercularis 2097 1417.664
- 19 2019 parsorbitalis 1361 918.504
- 20 2020 parstriangularis 2784 1843.752
- 21 2021 pericalcarine 2638 1805.453
- 22 2022 postcentral 7713 4966.229
- 23 2023 posteriorcingulate 2503 1716.131
- 24 2024 precentral 9841 6472.066
- 25 2025 precuneus 7647 5166.704
- 26 2026 rostralanteriorcingulate 1460 975.283
- 27 2027 rostralmiddlefrontal 11762 8062.871
- 28 2028 superiorfrontal 13951 9490.628
- 29 2029 superiorparietal 9841 6412.687
- 30 2030 superiortemporal 6693 4451.472
- 31 2031 supramarginal 6577 4376.953
- 32 2032 frontalpole 559 379.694
- 33 2033 temporalpole 754 536.237
- 34 2034 transversetemporal 591 366.553
- 35 2035 insula 3899 2599.391
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 23:15:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 1610 1110 3092 2.880 0.441 0.118 0.027 14 1.8 bankssts
- 1502 1063 3240 2.787 0.712 0.158 0.065 39 4.7 caudalanteriorcingulate
- 3799 2611 7981 2.728 0.455 0.130 0.037 48 5.9 caudalmiddlefrontal
- 2768 1818 4177 2.055 0.434 0.164 0.058 49 6.7 cuneus
- 486 369 1741 3.642 0.638 0.143 0.050 4 1.0 entorhinal
- 6320 4273 13576 2.664 0.580 0.145 0.079 180 12.5 fusiform
- 11478 7684 21958 2.515 0.527 0.142 0.045 186 19.9 inferiorparietal
- 5811 3928 11520 2.455 0.710 0.149 0.063 125 14.8 inferiortemporal
- 1736 1132 3208 2.529 0.808 0.156 0.075 36 4.4 isthmuscingulate
- 9606 6133 15622 2.211 0.468 0.143 0.051 169 19.6 lateraloccipital
- 4897 3264 9898 2.687 0.698 0.149 0.061 89 12.1 lateralorbitofrontal
- 4996 3427 7828 2.146 0.516 0.158 0.072 92 11.8 lingual
- 2949 1973 5355 2.358 0.590 0.167 0.083 100 10.2 medialorbitofrontal
- 5856 4038 14461 2.879 0.637 0.135 0.044 98 10.1 middletemporal
- 1110 766 2406 2.744 0.618 0.138 0.053 15 2.4 parahippocampal
- 3361 2176 6071 2.540 0.533 0.122 0.033 33 4.6 paracentral
- 2097 1418 4645 2.841 0.438 0.124 0.036 23 3.0 parsopercularis
- 1361 919 3215 2.716 0.485 0.163 0.064 30 2.9 parsorbitalis
- 2784 1844 5152 2.508 0.388 0.132 0.040 40 4.6 parstriangularis
- 2638 1805 3496 2.021 0.392 0.129 0.036 28 3.7 pericalcarine
- 7713 4966 12208 2.182 0.563 0.117 0.033 79 11.3 postcentral
- 2503 1716 4944 2.554 0.696 0.154 0.051 53 4.9 posteriorcingulate
- 9841 6472 19598 2.729 0.564 0.117 0.033 99 13.4 precentral
- 7647 5167 13732 2.451 0.543 0.140 0.048 122 14.8 precuneus
- 1460 975 3341 2.920 0.624 0.149 0.087 31 3.1 rostralanteriorcingulate
- 11762 8063 22493 2.393 0.525 0.161 0.066 289 28.9 rostralmiddlefrontal
- 13951 9491 30200 2.750 0.524 0.139 0.043 210 24.0 superiorfrontal
- 9841 6413 16008 2.237 0.447 0.130 0.039 135 14.9 superiorparietal
- 6693 4451 15382 2.996 0.615 0.119 0.035 70 9.9 superiortemporal
- 6577 4377 12969 2.637 0.492 0.140 0.043 103 11.1 supramarginal
- 559 380 1318 2.561 0.551 0.194 0.074 16 1.7 frontalpole
- 754 536 2343 3.120 0.936 0.182 0.106 25 3.5 temporalpole
- 591 367 1191 2.796 0.341 0.131 0.038 7 0.9 transversetemporal
- 3899 2599 8105 2.984 0.698 0.133 0.059 84 9.1 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 23:16:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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...
- 2 labels changed using aseg
- relabeling using gibbs priors...
- 000: 11829 changed, 169645 examined...
- 001: 2876 changed, 45320 examined...
- 002: 908 changed, 14566 examined...
- 003: 403 changed, 5107 examined...
- 004: 203 changed, 2193 examined...
- 005: 109 changed, 1151 examined...
- 006: 64 changed, 629 examined...
- 007: 35 changed, 326 examined...
- 008: 13 changed, 174 examined...
- 009: 10 changed, 84 examined...
- 010: 10 changed, 57 examined...
- 011: 6 changed, 57 examined...
- 012: 2 changed, 30 examined...
- 013: 1 changed, 8 examined...
- 014: 2 changed, 8 examined...
- 015: 3 changed, 9 examined...
- 016: 0 changed, 12 examined...
- 1 labels changed using aseg
- 000: 351 total segments, 269 labels (3338 vertices) changed
- 001: 109 total segments, 27 labels (122 vertices) changed
- 002: 84 total segments, 2 labels (21 vertices) changed
- 003: 82 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 135 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1158 vertices marked for relabeling...
- 1158 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 31 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 23:17:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 1199 831 2236 2.263 0.468 0.185 0.089 42 3.8 G_and_S_frontomargin
- 1656 1085 3232 2.411 0.561 0.147 0.044 25 3.0 G_and_S_occipital_inf
- 1833 1157 3543 2.487 0.591 0.119 0.041 18 3.7 G_and_S_paracentral
- 1730 1138 3512 2.629 0.514 0.132 0.038 23 2.8 G_and_S_subcentral
- 1574 1073 3401 2.415 0.579 0.206 0.107 59 6.1 G_and_S_transv_frontopol
- 3773 2524 7296 2.687 0.520 0.128 0.054 50 6.3 G_and_S_cingul-Ant
- 2081 1483 4625 2.905 0.459 0.135 0.037 32 3.2 G_and_S_cingul-Mid-Ant
- 2469 1657 4938 2.706 0.500 0.134 0.038 31 4.1 G_and_S_cingul-Mid-Post
- 863 584 2251 3.051 0.438 0.181 0.072 26 2.3 G_cingul-Post-dorsal
- 426 278 1075 2.945 0.541 0.204 0.149 16 2.2 G_cingul-Post-ventral
- 2491 1657 3713 1.996 0.442 0.167 0.061 46 6.1 G_cuneus
- 1211 820 3408 3.060 0.352 0.137 0.042 17 2.0 G_front_inf-Opercular
- 464 303 1078 2.642 0.402 0.154 0.051 11 1.0 G_front_inf-Orbital
- 1099 738 2650 2.725 0.312 0.157 0.055 24 2.5 G_front_inf-Triangul
- 5717 3978 14339 2.705 0.517 0.173 0.066 161 14.7 G_front_middle
- 9273 6277 22609 2.836 0.538 0.154 0.054 196 19.9 G_front_sup
- 766 497 1955 3.323 0.626 0.145 0.085 39 1.9 G_Ins_lg_and_S_cent_ins
- 898 609 2528 3.344 0.578 0.152 0.062 17 2.4 G_insular_short
- 3590 2264 7000 2.455 0.437 0.156 0.058 75 8.1 G_occipital_middle
- 2027 1268 3514 2.267 0.434 0.139 0.056 40 3.5 G_occipital_sup
- 2729 1779 6586 2.830 0.523 0.158 0.057 56 6.5 G_oc-temp_lat-fusifor
- 3008 2064 5328 2.206 0.566 0.179 0.091 73 8.7 G_oc-temp_med-Lingual
- 1454 1014 4481 3.391 0.722 0.156 0.067 23 3.8 G_oc-temp_med-Parahip
- 3246 2159 8014 2.839 0.695 0.173 0.075 85 10.3 G_orbital
- 4420 2968 10700 2.695 0.605 0.158 0.054 99 9.2 G_pariet_inf-Angular
- 3492 2323 8005 2.740 0.473 0.154 0.050 75 6.4 G_pariet_inf-Supramar
- 3233 2099 5997 2.299 0.434 0.138 0.039 54 5.1 G_parietal_sup
- 2762 1703 5058 2.335 0.456 0.127 0.035 35 4.0 G_postcentral
- 3697 2341 9230 3.045 0.461 0.123 0.037 49 5.1 G_precentral
- 2940 1987 6751 2.638 0.507 0.147 0.048 59 5.8 G_precuneus
- 579 403 1267 2.267 0.664 0.240 0.160 43 3.6 G_rectus
- 606 405 1196 2.541 0.870 0.105 0.053 8 1.5 G_subcallosal
- 480 291 1063 2.951 0.375 0.145 0.042 7 0.8 G_temp_sup-G_T_transv
- 2298 1478 6917 3.322 0.515 0.143 0.047 39 4.6 G_temp_sup-Lateral
- 1009 687 2589 3.153 0.703 0.122 0.052 19 2.6 G_temp_sup-Plan_polar
- 984 699 2168 2.802 0.487 0.117 0.026 7 1.1 G_temp_sup-Plan_tempo
- 3150 2099 7184 2.523 0.821 0.175 0.086 98 11.3 G_temporal_inf
- 3362 2298 10004 3.092 0.602 0.152 0.058 78 7.5 G_temporal_middle
- 578 380 899 2.421 0.401 0.102 0.021 4 0.6 Lat_Fis-ant-Horizont
- 219 155 373 2.633 0.479 0.096 0.026 1 0.2 Lat_Fis-ant-Vertical
- 1656 1102 2440 2.483 0.510 0.115 0.032 11 2.2 Lat_Fis-post
- 4572 2897 6639 1.997 0.418 0.151 0.059 90 11.4 Pole_occipital
- 1950 1380 5551 3.005 0.687 0.171 0.083 53 6.3 Pole_temporal
- 3051 2090 4282 2.247 0.565 0.133 0.047 37 5.4 S_calcarine
- 3677 2459 4755 2.107 0.705 0.107 0.030 24 4.8 S_central
- 1698 1147 2501 2.310 0.454 0.125 0.038 19 2.4 S_cingul-Marginalis
- 676 456 1194 2.725 0.553 0.104 0.024 3 0.7 S_circular_insula_ant
- 1466 971 2401 2.737 0.553 0.092 0.029 7 2.0 S_circular_insula_inf
- 1747 1163 2622 2.591 0.404 0.105 0.027 10 2.0 S_circular_insula_sup
- 1340 951 2179 2.361 0.483 0.115 0.030 12 1.8 S_collat_transv_ant
- 815 538 1150 2.232 0.371 0.126 0.037 7 1.2 S_collat_transv_post
- 2327 1584 3739 2.319 0.444 0.128 0.040 33 3.6 S_front_inf
- 3348 2232 4732 2.214 0.404 0.129 0.039 42 5.2 S_front_middle
- 2969 2074 5133 2.543 0.406 0.123 0.035 30 4.0 S_front_sup
- 1000 675 1282 2.163 0.386 0.112 0.025 6 1.1 S_interm_prim-Jensen
- 4107 2757 5883 2.263 0.439 0.128 0.042 49 6.0 S_intrapariet_and_P_trans
- 1628 1102 2199 2.127 0.382 0.135 0.032 15 2.2 S_oc_middle_and_Lunatus
- 1504 995 1987 2.046 0.379 0.107 0.023 11 1.4 S_oc_sup_and_transversal
- 915 608 1478 2.392 0.444 0.109 0.028 10 0.9 S_occipital_ant
- 1119 769 1819 2.321 0.494 0.135 0.211 93 1.8 S_oc-temp_lat
- 2333 1622 3685 2.414 0.386 0.108 0.028 15 2.5 S_oc-temp_med_and_Lingual
- 710 472 890 2.150 0.320 0.132 0.054 6 1.1 S_orbital_lateral
- 850 599 1306 2.320 0.791 0.115 0.042 9 0.9 S_orbital_med-olfact
- 1944 1290 3332 2.539 0.512 0.151 0.054 30 4.1 S_orbital-H_Shaped
- 3147 2075 4465 2.272 0.501 0.131 0.038 34 5.0 S_parieto_occipital
- 2093 1368 2621 2.156 0.865 0.149 0.067 46 6.1 S_pericallosal
- 2900 1919 4031 2.196 0.436 0.114 0.031 25 3.8 S_postcentral
- 1963 1307 3068 2.637 0.367 0.117 0.029 17 2.4 S_precentral-inf-part
- 2345 1586 3589 2.362 0.419 0.102 0.024 15 2.4 S_precentral-sup-part
- 402 265 542 2.059 0.517 0.165 0.055 7 0.9 S_suborbital
- 1593 1093 2476 2.302 0.331 0.128 0.037 18 2.4 S_subparietal
- 1807 1233 2434 2.221 0.531 0.107 0.023 11 1.8 S_temporal_inf
- 7570 5149 12736 2.654 0.511 0.118 0.030 68 9.3 S_temporal_sup
- 348 237 629 2.852 0.431 0.132 0.031 3 0.5 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 23:18:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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: 3255 changed, 169645 examined...
- 001: 750 changed, 13958 examined...
- 002: 161 changed, 4001 examined...
- 003: 62 changed, 952 examined...
- 004: 22 changed, 367 examined...
- 005: 10 changed, 126 examined...
- 006: 7 changed, 61 examined...
- 007: 4 changed, 45 examined...
- 008: 3 changed, 24 examined...
- 009: 1 changed, 19 examined...
- 010: 1 changed, 7 examined...
- 011: 1 changed, 9 examined...
- 012: 2 changed, 5 examined...
- 013: 3 changed, 10 examined...
- 014: 2 changed, 13 examined...
- 015: 2 changed, 14 examined...
- 016: 2 changed, 14 examined...
- 017: 2 changed, 13 examined...
- 018: 2 changed, 10 examined...
- 019: 2 changed, 15 examined...
- 020: 4 changed, 14 examined...
- 021: 1 changed, 16 examined...
- 022: 2 changed, 7 examined...
- 023: 3 changed, 8 examined...
- 024: 2 changed, 15 examined...
- 025: 2 changed, 11 examined...
- 026: 3 changed, 14 examined...
- 027: 0 changed, 11 examined...
- 132 labels changed using aseg
- 000: 70 total segments, 37 labels (189 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 46 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1079 vertices marked for relabeling...
- 1079 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 18 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 23:19:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 1508 1064 3233 2.777 0.723 0.158 0.065 39 4.7 caudalanteriorcingulate
- 4034 2755 8209 2.711 0.452 0.128 0.037 49 6.1 caudalmiddlefrontal
- 3476 2303 5187 2.072 0.415 0.156 0.052 55 7.6 cuneus
- 483 370 1752 3.672 0.631 0.145 0.051 5 1.0 entorhinal
- 5673 3810 12223 2.695 0.566 0.144 0.081 167 11.1 fusiform
- 10541 7050 20164 2.500 0.531 0.141 0.045 168 18.0 inferiorparietal
- 6462 4380 12924 2.462 0.705 0.150 0.063 143 16.3 inferiortemporal
- 1799 1173 3268 2.510 0.806 0.153 0.073 36 4.4 isthmuscingulate
- 10121 6449 16464 2.214 0.467 0.143 0.051 178 20.5 lateraloccipital
- 5262 3516 10471 2.630 0.714 0.160 0.068 111 14.6 lateralorbitofrontal
- 5011 3441 7881 2.148 0.516 0.157 0.071 91 11.7 lingual
- 2424 1646 4749 2.355 0.694 0.177 0.094 94 9.7 medialorbitofrontal
- 7140 4914 16799 2.874 0.616 0.133 0.042 111 11.9 middletemporal
- 1098 757 2352 2.708 0.609 0.138 0.052 15 2.3 parahippocampal
- 3515 2296 6431 2.539 0.529 0.124 0.033 35 4.8 paracentral
- 2144 1457 4679 2.827 0.437 0.122 0.035 23 3.1 parsopercularis
- 1472 990 3219 2.642 0.492 0.144 0.056 26 2.7 parsorbitalis
- 2990 1979 5362 2.466 0.416 0.134 0.040 42 5.2 parstriangularis
- 2641 1806 3515 2.027 0.390 0.131 0.038 29 3.9 pericalcarine
- 8196 5292 12923 2.180 0.562 0.117 0.034 84 11.9 postcentral
- 2669 1825 5537 2.622 0.691 0.155 0.052 56 5.5 posteriorcingulate
- 9377 6146 19002 2.753 0.561 0.119 0.034 97 13.1 precentral
- 7636 5155 13856 2.451 0.547 0.140 0.048 123 14.7 precuneus
- 1666 1103 3530 2.825 0.635 0.148 0.081 33 3.5 rostralanteriorcingulate
- 7457 5068 14428 2.450 0.508 0.155 0.058 162 16.6 rostralmiddlefrontal
- 18386 12561 38768 2.659 0.543 0.145 0.050 335 34.9 superiorfrontal
- 8370 5453 13730 2.253 0.453 0.131 0.040 118 12.9 superiorparietal
- 8815 5906 20569 2.989 0.636 0.127 0.043 119 16.5 superiortemporal
- 6446 4301 12618 2.630 0.491 0.141 0.043 103 10.8 supramarginal
- 584 361 1177 2.802 0.333 0.131 0.038 7 0.9 transversetemporal
- 3560 2397 7458 2.959 0.675 0.130 0.052 68 7.1 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 23:20:09 CEST 2013
- bbregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.log
- Thu Aug 8 23:20:09 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998757, 0.0408089, 0.02861)
- j_ras = (0.0441177, 0.99097, 0.126615)
- k_ras = (0.0231846, -0.12772, 0.991539)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii...
- fslregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fslregister.log
- Thu Aug 8 23:20:14 CEST 2013
- --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.16415e-09, 1.86265e-09)
- j_ras = (-1.86265e-09, 1.49012e-08, -1)
- k_ras = (9.31323e-10, 1, -1.49012e-08)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998757, 0.0408089, 0.02861)
- j_ras = (0.0441177, 0.99097, 0.126615)
- k_ras = (0.0231846, -0.12772, 0.991539)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311076
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0 --s sub006 --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/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.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/sub006/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/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.889;
- 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) --------
- 0.999 -0.041 -0.029 -0.000;
- 0.023 -0.128 0.992 -0.000;
- -0.044 -0.991 -0.127 0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 -0.041 -0.029 -0.000;
- 0.023 -0.128 0.992 -0.000;
- -0.044 -0.991 -0.127 0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub006
- RegMat ---------------------------
- 0.999 -0.041 -0.029 -0.000;
- 0.023 -0.128 0.992 -0.000;
- -0.044 -0.991 -0.127 0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311076, ref det = -1
- Thu Aug 8 23:20:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0
- Thu Aug 8 23:24:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.999 -0.042 -0.020 40.136;
- -0.025 -0.120 -0.992 274.192;
- 0.039 0.992 -0.121 12.050;
- 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/sub006/mri/transforms/tmp.bbregister.19132/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/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/sub006/mri/transforms/tmp.bbregister.19132/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.889;
- 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 = -0.311076, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.999 -0.039 -0.025 0.009;
- 0.020 -0.121 0.992 1.308;
- -0.042 -0.992 -0.120 -0.930;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 -0.039 -0.025 0.009;
- 0.020 -0.121 0.992 1.308;
- -0.042 -0.992 -0.120 -0.930;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub006
- RegMat ---------------------------
- 0.999 -0.039 -0.025 0.009;
- 0.020 -0.121 0.992 1.308;
- -0.042 -0.992 -0.120 -0.930;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 23:20:14 CEST 2013
- Ended at Thu Aug 8 23:31:25 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat
- subject sub006
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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 1376052073
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 -0.039 -0.025 0.009;
- 0.020 -0.121 0.992 1.308;
- -0.042 -0.992 -0.120 -0.930;
- 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 0.990036
- 1 -25.0 -25.0 25.0 1.013869
- 2 -25.0 25.0 -25.0 1.045360
- 3 -25.0 25.0 25.0 1.003149
- 4 25.0 -25.0 -25.0 1.023281
- 5 25.0 -25.0 25.0 1.006686
- 6 25.0 25.0 -25.0 1.010024
- 7 25.0 25.0 25.0 1.048604
- REL: 8 0.322576 8.141011 1.017626 rel = 0.316989
- Initial costs ----------------
- Number of surface hits 3238
- WM Intensity 61.7561 +/- 11.7398
- Ctx Intensity 77.7046 +/- 15.1309
- Pct Contrast 22.3549 +/- 23.0208
- Cost 0.3226
- RelCost 0.3170
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9854 0.9854 0.0
- 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9791 0.9791 0.0
- 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9606 0.9606 0.0
- 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9556 0.9556 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8671 0.8671 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8189 0.8189 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7643 0.7643 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6566 0.6566 0.0
- 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6078 0.6078 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3226 0.3226 0.0
- Brute Force --------------------------
- Min cost was 0.322576
- Number of iterations 729
- Search time 2.528000 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 -0.006 0.000 0.000 0.000 0.000 0.000 0.3225513539
- 11 -0.005 0.000 0.000 0.000 0.000 0.000 0.3225499366
- 15 -0.005 -1.618 0.000 0.000 0.000 0.000 0.1223710691
- 20 -0.005 -1.431 0.000 0.000 0.000 0.000 0.1196453081
- 21 -0.005 -1.460 0.000 0.000 0.000 0.000 0.1190840389
- 22 -0.005 -1.491 0.000 0.000 0.000 0.000 0.1184857389
- 24 -0.005 -1.500 0.000 0.000 0.000 0.000 0.1184697786
- 25 -0.005 -1.498 0.000 0.000 0.000 0.000 0.1184583008
- 26 -0.005 -1.496 0.000 0.000 0.000 0.000 0.1184563610
- 29 -0.005 -1.496 1.000 0.000 0.000 0.000 0.1170204377
- 33 -0.005 -1.496 0.618 0.000 0.000 0.000 0.0877717013
- 35 -0.005 -1.496 0.524 0.000 0.000 0.000 0.0860064007
- 36 -0.005 -1.496 0.509 0.000 0.000 0.000 0.0859274583
- 38 -0.005 -1.496 0.507 0.000 0.000 0.000 0.0859264095
- 48 -0.005 -1.496 0.507 -0.064 0.000 0.000 0.0855856668
- 49 -0.005 -1.496 0.507 -0.038 0.000 0.000 0.0849571324
- 59 -0.005 -1.496 0.507 -0.038 -0.082 0.000 0.0845974589
- 60 -0.005 -1.496 0.507 -0.038 -0.052 0.000 0.0843965611
- 61 -0.005 -1.496 0.507 -0.038 -0.051 0.000 0.0843894536
- 62 -0.005 -1.496 0.507 -0.038 -0.032 0.000 0.0843761775
- 63 -0.005 -1.496 0.507 -0.038 -0.040 0.000 0.0843609554
- 64 -0.005 -1.496 0.507 -0.038 -0.039 0.000 0.0843584762
- 65 -0.005 -1.496 0.507 -0.038 -0.037 0.000 0.0843576955
- 74 -0.005 -1.496 0.507 -0.038 -0.037 0.119 0.0818356881
- 76 -0.005 -1.496 0.507 -0.038 -0.037 0.104 0.0817269000
- 79 -0.005 -1.496 0.507 -0.038 -0.037 0.098 0.0817165227
- 89 0.062 -1.496 0.507 -0.038 -0.037 0.098 0.0784200867
- 91 0.079 -1.496 0.507 -0.038 -0.037 0.098 0.0783580601
- 92 0.076 -1.496 0.507 -0.038 -0.037 0.098 0.0783375078
- 93 0.074 -1.496 0.507 -0.038 -0.037 0.098 0.0783332821
- 102 0.074 -1.500 0.507 -0.038 -0.037 0.098 0.0782613848
- 104 0.074 -1.532 0.507 -0.038 -0.037 0.098 0.0782124181
- 105 0.074 -1.518 0.507 -0.038 -0.037 0.098 0.0781260750
- 106 0.074 -1.519 0.507 -0.038 -0.037 0.098 0.0781256759
- 114 0.074 -1.519 0.518 -0.038 -0.037 0.098 0.0780031421
- 116 0.074 -1.519 0.528 -0.038 -0.037 0.098 0.0779685306
- 117 0.074 -1.519 0.530 -0.038 -0.037 0.098 0.0779660198
- 128 0.074 -1.519 0.530 -0.079 -0.037 0.098 0.0775032375
- 129 0.074 -1.519 0.530 -0.070 -0.037 0.098 0.0773934281
- 130 0.074 -1.519 0.530 -0.066 -0.037 0.098 0.0773850494
- 140 0.074 -1.519 0.530 -0.066 -0.045 0.098 0.0772513331
- 142 0.074 -1.519 0.530 -0.066 -0.049 0.098 0.0772355263
- 151 0.074 -1.519 0.530 -0.066 -0.049 0.153 0.0768815185
- 152 0.074 -1.519 0.530 -0.066 -0.049 0.144 0.0767667536
- 153 0.074 -1.519 0.530 -0.066 -0.049 0.133 0.0767352155
- 154 0.074 -1.519 0.530 -0.066 -0.049 0.136 0.0767350124
- 156 0.074 -1.519 0.530 -0.066 -0.049 0.135 0.0767345098
- 157 0.153 -1.542 0.554 -0.094 -0.061 0.171 0.0757315281
- 165 0.156 -1.543 0.555 -0.096 -0.062 0.173 0.0757278872
- 166 0.160 -1.544 0.556 -0.097 -0.062 0.175 0.0757259927
- 169 0.160 -1.544 0.556 -0.097 -0.062 0.175 0.0757256658
- 177 0.160 -1.544 0.556 -0.097 -0.062 0.204 0.0755171844
- 179 0.160 -1.544 0.556 -0.097 -0.062 0.196 0.0755028243
- 181 0.160 -1.544 0.556 -0.097 -0.062 0.199 0.0754996383
- 190 0.160 -1.513 0.556 -0.097 -0.062 0.199 0.0746624075
- 191 0.160 -1.464 0.556 -0.097 -0.062 0.199 0.0746055559
- 193 0.160 -1.487 0.556 -0.097 -0.062 0.199 0.0744588357
- 195 0.160 -1.489 0.556 -0.097 -0.062 0.199 0.0744576947
- 206 0.160 -1.489 0.566 -0.097 -0.062 0.199 0.0743555643
- 207 0.160 -1.489 0.571 -0.097 -0.062 0.199 0.0743416053
- 219 0.160 -1.489 0.571 -0.102 -0.062 0.199 0.0743244867
- 229 0.160 -1.489 0.571 -0.102 -0.054 0.199 0.0742840259
- 232 0.160 -1.489 0.571 -0.102 -0.055 0.199 0.0742834399
- 239 0.190 -1.498 0.580 -0.112 -0.059 0.213 0.0741403009
- 242 0.209 -1.503 0.586 -0.119 -0.062 0.221 0.0741398050
- 244 0.209 -1.503 0.586 -0.119 -0.062 0.221 0.0741395840
- 247 0.211 -1.504 0.586 -0.120 -0.063 0.222 0.0741395027
- 248 0.210 -1.503 0.586 -0.120 -0.062 0.222 0.0741393948
- 249 0.210 -1.503 0.586 -0.120 -0.062 0.222 0.0741393463
- 259 0.210 -1.503 0.586 -0.120 -0.062 0.233 0.0738855742
- 261 0.210 -1.503 0.586 -0.120 -0.062 0.248 0.0737759217
- 262 0.210 -1.503 0.586 -0.120 -0.062 0.246 0.0737721810
- 273 0.210 -1.490 0.586 -0.120 -0.062 0.246 0.0736963995
- 285 0.210 -1.490 0.587 -0.120 -0.062 0.246 0.0736915133
- 286 0.210 -1.490 0.592 -0.120 -0.062 0.246 0.0736834938
- 288 0.210 -1.490 0.591 -0.120 -0.062 0.246 0.0736833623
- 298 0.210 -1.490 0.591 -0.111 -0.062 0.246 0.0735968226
- 300 0.210 -1.490 0.591 -0.107 -0.062 0.246 0.0735963327
- 302 0.210 -1.490 0.591 -0.108 -0.062 0.246 0.0735944569
- 303 0.210 -1.490 0.591 -0.109 -0.062 0.246 0.0735940538
- 311 0.210 -1.490 0.591 -0.109 -0.070 0.246 0.0735228430
- 312 0.210 -1.490 0.591 -0.109 -0.074 0.246 0.0735080376
- 315 0.210 -1.490 0.591 -0.109 -0.075 0.246 0.0735077031
- 321 0.240 -1.498 0.599 -0.120 -0.080 0.260 0.0734949468
- 322 0.226 -1.494 0.595 -0.115 -0.078 0.254 0.0734300529
- 324 0.228 -1.495 0.596 -0.116 -0.078 0.255 0.0734286940
- 327 0.228 -1.495 0.596 -0.116 -0.078 0.255 0.0734286205
- 338 0.228 -1.495 0.596 -0.116 -0.078 0.253 0.0734281123
- 348 0.228 -1.479 0.596 -0.116 -0.078 0.253 0.0734006223
- 349 0.228 -1.482 0.596 -0.116 -0.078 0.253 0.0733844990
- 350 0.228 -1.486 0.596 -0.116 -0.078 0.253 0.0733790100
- 362 0.228 -1.486 0.592 -0.116 -0.078 0.253 0.0733697099
- 364 0.228 -1.486 0.593 -0.116 -0.078 0.253 0.0733696556
- 374 0.228 -1.486 0.593 -0.110 -0.078 0.253 0.0733206040
- 376 0.228 -1.486 0.593 -0.105 -0.078 0.253 0.0733125478
- 377 0.228 -1.486 0.593 -0.107 -0.078 0.253 0.0733110118
- 387 0.228 -1.486 0.593 -0.107 -0.083 0.253 0.0732951888
- 396 0.232 -1.487 0.595 -0.108 -0.083 0.255 0.0732732502
- 397 0.237 -1.488 0.596 -0.110 -0.084 0.257 0.0732630673
- 398 0.238 -1.488 0.596 -0.110 -0.084 0.258 0.0732627839
- 399 0.238 -1.488 0.596 -0.110 -0.084 0.257 0.0732624241
- 403 0.247 -1.482 0.597 -0.104 -0.090 0.260 0.0732474931
- 437 0.238 -1.483 0.592 -0.110 -0.084 0.259 0.0732438122
- 439 0.238 -1.483 0.590 -0.110 -0.084 0.259 0.0732404503
- 449 0.238 -1.483 0.590 -0.108 -0.084 0.259 0.0732309201
- 451 0.238 -1.483 0.590 -0.105 -0.084 0.259 0.0732277520
- 452 0.238 -1.483 0.590 -0.106 -0.084 0.259 0.0732268628
- 462 0.238 -1.483 0.590 -0.106 -0.083 0.259 0.0732261879
- 471 0.241 -1.484 0.590 -0.107 -0.084 0.260 0.0732203038
- 472 0.242 -1.484 0.591 -0.108 -0.084 0.260 0.0732202274
- 481 0.245 -1.480 0.585 -0.105 -0.083 0.263 0.0732121668
- 527 0.242 -1.483 0.588 -0.105 -0.084 0.260 0.0732108126
- 547 0.243 -1.483 0.589 -0.106 -0.084 0.261 0.0732097022
- 549 0.243 -1.483 0.589 -0.106 -0.084 0.261 0.0732096414
- 551 0.244 -1.482 0.587 -0.104 -0.084 0.262 0.0732042478
- 556 0.245 -1.481 0.586 -0.103 -0.084 0.262 0.0732030385
- 559 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732029930
- 561 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732029320
- 562 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732029164
- 564 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732028100
- 577 0.245 -1.481 0.585 -0.103 -0.084 0.264 0.0732018670
- Powell done niters = 7
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.013482
- 1 -25.0 -25.0 25.0 1.015559
- 2 -25.0 25.0 -25.0 1.034208
- 3 -25.0 25.0 25.0 1.000666
- 4 25.0 -25.0 -25.0 1.034182
- 5 25.0 -25.0 25.0 0.991798
- 6 25.0 25.0 -25.0 1.006023
- 7 25.0 25.0 25.0 1.034180
- REL: 8 0.073202 8.130098 1.016262 rel = 0.0720305
- Number of iterations 7
- Min cost was 0.073202
- Number of FunctionCalls 641
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 2.591000 sec
- Parameters at optimum (transmm) 0.24532 -1.48124 0.58539
- Parameters at optimum (rotdeg) -0.10298 -0.08425 0.26413
- Final costs ----------------
- Number of surface hits 3238
- WM Intensity 60.0746 +/- 10.5131
- Ctx Intensity 78.1624 +/- 10.7433
- Pct Contrast 26.4330 +/- 15.2985
- Cost 0.0732
- RelCost 0.3170
- Reg at min cost was
- 0.999 -0.037 -0.029 0.250;
- 0.024 -0.123 0.992 -0.175;
- -0.040 -0.992 -0.122 -0.347;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat, type = 14
- Original Reg
- 0.999 -0.039 -0.025 0.009;
- 0.020 -0.121 0.992 1.308;
- -0.042 -0.992 -0.120 -0.930;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.002 0.004 -0.241;
- -0.005 0.002 0.000 1.483;
- -0.001 -0.000 0.002 -0.583;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.655014
- Computing change in rh position
- Surface RMS Diff (mm) 1.549561 1.872015
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat
- subject sub006
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1376539157
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 -0.037 -0.029 0.250;
- 0.024 -0.123 0.992 -0.175;
- -0.040 -0.992 -0.122 -0.347;
- 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 1.000144
- 1 -25.0 -25.0 25.0 1.011963
- 2 -25.0 25.0 -25.0 1.028762
- 3 -25.0 25.0 25.0 1.017444
- 4 25.0 -25.0 -25.0 1.023030
- 5 25.0 -25.0 25.0 1.003200
- 6 25.0 25.0 -25.0 1.006099
- 7 25.0 25.0 25.0 1.018704
- REL: 8 0.074000 8.109344 1.013668 rel = 0.0730019
- Initial costs ----------------
- Number of surface hits 323295
- WM Intensity 60.0945 +/- 10.4129
- Ctx Intensity 78.3960 +/- 10.7337
- Pct Contrast 26.6644 +/- 15.2882
- Cost 0.0740
- RelCost 0.0730
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0884 0.0884 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0860 0.0860 0.0
- 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0824 0.0824 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0789 0.0789 0.0
- 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.0775 0.0775 0.0
- 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0762 0.0762 0.0
- 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0755 0.0755 0.0
- 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0755 0.0755 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0732 0.0732 0.0
- Brute Force --------------------------
- Min cost was 0.073202
- Number of iterations 729
- Search time 2.842000 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 -0.011 0.000 0.000 0.000 0.000 0.000 0.0739579968
- 8 -0.023 0.000 0.000 0.000 0.000 0.000 0.0739393766
- 10 -0.024 0.000 0.000 0.000 0.000 0.000 0.0739391684
- 18 -0.024 0.068 0.000 0.000 0.000 0.000 0.0736410288
- 19 -0.024 0.054 0.000 0.000 0.000 0.000 0.0736210929
- 28 -0.024 0.054 0.144 0.000 0.000 0.000 0.0712034427
- 29 -0.024 0.054 0.145 0.000 0.000 0.000 0.0712014029
- 30 -0.024 0.054 0.154 0.000 0.000 0.000 0.0711957153
- 32 -0.024 0.054 0.152 0.000 0.000 0.000 0.0711948811
- 42 -0.024 0.054 0.152 0.003 0.000 0.000 0.0711937157
- 51 -0.024 0.054 0.152 0.003 -0.021 0.000 0.0710840807
- 52 -0.024 0.054 0.152 0.003 -0.028 0.000 0.0710745386
- 55 -0.024 0.054 0.152 0.003 -0.029 0.000 0.0710742340
- 63 -0.024 0.054 0.152 0.003 -0.029 0.003 0.0710718816
- 65 -0.024 0.054 0.152 0.003 -0.029 0.005 0.0710714752
- 66 -0.024 0.054 0.152 0.003 -0.029 0.006 0.0710712416
- 77 -0.013 0.054 0.152 0.003 -0.029 0.006 0.0710605916
- 87 -0.013 0.055 0.152 0.003 -0.029 0.006 0.0710605245
- 96 -0.013 0.055 0.154 0.003 -0.029 0.006 0.0710602217
- 106 -0.013 0.055 0.154 0.004 -0.029 0.006 0.0710595122
- 115 -0.013 0.055 0.154 0.004 -0.031 0.006 0.0710593576
- 124 -0.013 0.055 0.154 0.004 -0.031 0.010 0.0710563353
- 126 -0.013 0.055 0.154 0.004 -0.031 0.011 0.0710561702
- 127 -0.013 0.055 0.154 0.004 -0.031 0.012 0.0710560869
- 130 -0.003 0.056 0.156 0.006 -0.032 0.018 0.0710552827
- 136 -0.007 0.056 0.155 0.005 -0.032 0.016 0.0710535106
- 137 -0.008 0.056 0.155 0.005 -0.031 0.015 0.0710534580
- 138 -0.008 0.056 0.155 0.005 -0.031 0.016 0.0710533858
- 162 -0.008 0.057 0.155 0.005 -0.031 0.016 0.0710532018
- 171 -0.008 0.057 0.152 0.005 -0.031 0.016 0.0710519125
- 198 -0.006 0.057 0.153 0.005 -0.032 0.016 0.0710517517
- 199 -0.006 0.057 0.153 0.005 -0.032 0.016 0.0710517061
- 200 -0.007 0.057 0.152 0.005 -0.032 0.016 0.0710517012
- 203 -0.007 0.057 0.152 0.005 -0.032 0.016 0.0710516797
- 217 -0.007 0.057 0.152 0.005 -0.032 0.017 0.0710516335
- 270 -0.007 0.057 0.152 0.005 -0.032 0.017 0.0710516217
- Powell done niters = 4
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.000527
- 1 -25.0 -25.0 25.0 1.012389
- 2 -25.0 25.0 -25.0 1.028572
- 3 -25.0 25.0 25.0 1.018441
- 4 25.0 -25.0 -25.0 1.022629
- 5 25.0 -25.0 25.0 1.001609
- 6 25.0 25.0 -25.0 1.005235
- 7 25.0 25.0 25.0 1.020102
- REL: 8 0.071052 8.109503 1.013688 rel = 0.0700922
- Number of iterations 4
- Min cost was 0.071052
- Number of FunctionCalls 333
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 51.287000 sec
- Parameters at optimum (transmm) -0.00683 0.05697 0.15243
- Parameters at optimum (rotdeg) 0.00519 -0.03151 0.01697
- Final costs ----------------
- Number of surface hits 323295
- WM Intensity 60.0684 +/- 10.3946
- Ctx Intensity 78.3842 +/- 10.7444
- Pct Contrast 26.6871 +/- 15.2674
- Cost 0.0711
- RelCost 0.0730
- Reg at min cost was
- 0.999 -0.036 -0.029 0.243;
- 0.025 -0.123 0.992 -0.118;
- -0.040 -0.992 -0.122 -0.195;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.999 -0.037 -0.029 0.250;
- 0.024 -0.123 0.992 -0.175;
- -0.040 -0.992 -0.122 -0.347;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 -0.001 0.000 0.007;
- -0.000 -0.000 -0.000 -0.057;
- -0.001 0.000 -0.000 -0.153;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.153461
- Computing change in rh position
- Surface RMS Diff (mm) 0.170445 0.209095
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 --------
- 0.999 -0.036 -0.029 0.243;
- 0.025 -0.123 0.992 -0.118;
- -0.040 -0.992 -0.122 -0.195;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.889;
- 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 --------
- 0.999 -0.036 -0.029 0.243;
- 0.025 -0.123 0.992 -0.118;
- -0.040 -0.992 -0.122 -0.195;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub006
- RegMat ---------------------------
- 0.999 -0.036 -0.029 0.243;
- 0.025 -0.123 0.992 -0.118;
- -0.040 -0.992 -0.122 -0.195;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.005 0.001 -0.130;
- 0.005 1.000 0.005 -0.080;
- -0.001 -0.005 1.000 0.196;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.699 -0.026 -0.016 40.677;
- -0.021 -0.081 -0.661 273.305;
- 0.025 0.661 -0.082 13.122;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 23:20:09 CEST 2013
- Ended at Thu Aug 8 23:33:28 CEST 2013
- BBR-Run-Time-Sec 799
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998757, 0.0408089, 0.02861)
- j_ras = (0.0441177, 0.99097, 0.126615)
- k_ras = (0.0231846, -0.12772, 0.991539)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub006
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.005 0.001 -0.129;
- 0.005 1.000 0.005 -0.080;
- -0.001 -0.005 1.000 0.196;
- 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/sub006/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 14582 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/sub006/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub006 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/sub006/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- 24515 bright wm thresholded.
- 438 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig...
- computing class statistics...
- border white: 318128 voxels (1.90%)
- border gray 352780 voxels (2.10%)
- WM (93.0): 93.8 +- 10.2 [70.0 --> 110.0]
- GM (75.0) : 73.0 +- 13.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.3 (was 70)
- setting MAX_BORDER_WHITE to 116.2 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 29.7 (was 40)
- setting MAX_GRAY to 95.8 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=57
- mean inside = 93.4, mean outside = 67.5
- 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/sub006/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.03-->8.22) (max @ vno 73397 --> 77073)
- face area 0.33 +- 0.16 (0.00-->8.17)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 205 points - only 10.24% unknown
- deleting segment 2 with 22 points - only 0.00% unknown
- deleting segment 3 with 12 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 7 with 21 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 742 points - only 0.00% unknown
- deleting segment 11 with 12 points - only 0.00% unknown
- deleting segment 13 with 5 points - only 0.00% unknown
- deleting segment 15 with 38 points - only 0.00% unknown
- deleting segment 16 with 15 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 17 with 4 points - only 0.00% unknown
- deleting segment 18 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 19 with 3 points - only 0.00% unknown
- deleting segment 20 with 8 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 (0.09-->8.22) (max @ vno 77073 --> 73397)
- face area 0.33 +- 0.16 (0.00-->8.17)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5338815.5, rms=0.00
- rms = 1.34, 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=5338815.5, rms=0.000 (1.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 205 points - only 10.24% unknown
- deleting segment 2 with 22 points - only 0.00% unknown
- deleting segment 3 with 12 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 21 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 742 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 38 points - only 0.00% unknown
- deleting segment 11 with 15 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 12 with 4 points - only 0.00% unknown
- deleting segment 13 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- deleting segment 15 with 8 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-->8.22) (max @ vno 77073 --> 73397)
- face area 0.33 +- 0.16 (0.00-->8.17)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5338815.5, rms=0.00
- rms = 1.34, 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...
- 002: dt: 0.1250, sse=5338815.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 205 points - only 10.24% unknown
- deleting segment 2 with 22 points - only 0.00% unknown
- deleting segment 3 with 12 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 21 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 742 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 38 points - only 0.00% unknown
- deleting segment 11 with 15 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 12 with 4 points - only 0.00% unknown
- deleting segment 13 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- deleting segment 15 with 8 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-->8.22) (max @ vno 77073 --> 73397)
- face area 0.33 +- 0.16 (0.00-->8.17)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5338815.5, rms=0.00
- rms = 1.34, 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=5338815.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 205 points - only 10.24% unknown
- deleting segment 2 with 22 points - only 0.00% unknown
- deleting segment 3 with 12 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 21 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 742 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 38 points - only 0.00% unknown
- deleting segment 11 with 15 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 12 with 4 points - only 0.00% unknown
- deleting segment 13 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- deleting segment 15 with 8 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=5338815.5, rms=0.00
- rms = 1.34, 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...
- 004: dt: 0.1250, sse=5338815.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- removing 1 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 [101.60 232.40], gm=167.00+-21.80, and vertices in regions > 156.1
- 56865 surface locations found to contain inconsistent values (3318 in, 53547 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=585899.2, rms=0.24
- 001: dt: 0.5000, sse=552557.2, rms=0.233 (0.000%)
- 002: dt: 0.5000, sse=532313.9, rms=0.218 (0.000%)
- 003: dt: 0.5000, sse=520637.5, rms=0.207 (0.000%)
- 004: dt: 0.5000, sse=511675.7, rms=0.198 (0.000%)
- 005: dt: 0.5000, sse=505424.5, rms=0.189 (0.000%)
- 006: dt: 0.5000, sse=500991.1, rms=0.182 (0.000%)
- 007: dt: 0.5000, sse=498248.5, rms=0.175 (0.000%)
- 008: dt: 0.5000, sse=496290.6, rms=0.170 (0.000%)
- 009: dt: 0.5000, sse=494632.1, rms=0.165 (0.000%)
- 010: dt: 0.5000, sse=493524.8, rms=0.161 (0.000%)
- 011: dt: 0.5000, sse=492451.7, rms=0.158 (0.000%)
- 012: dt: 0.5000, sse=491455.6, rms=0.155 (0.000%)
- 013: dt: 0.5000, sse=490763.1, rms=0.153 (0.000%)
- 014: dt: 0.5000, sse=489956.1, rms=0.151 (0.000%)
- 015: dt: 0.5000, sse=489047.1, rms=0.149 (0.000%)
- 016: dt: 0.5000, sse=487979.8, rms=0.148 (0.000%)
- 017: dt: 0.5000, sse=486870.7, rms=0.146 (0.000%)
- 018: dt: 0.5000, sse=485633.1, rms=0.145 (0.000%)
- 019: dt: 0.5000, sse=484633.0, rms=0.145 (0.000%)
- 020: dt: 0.5000, sse=483442.2, rms=0.144 (0.000%)
- 021: dt: 0.5000, sse=482316.2, rms=0.144 (0.000%)
- 022: dt: 0.5000, sse=480975.9, rms=0.143 (0.000%)
- 023: dt: 0.5000, sse=479811.6, rms=0.143 (0.000%)
- 024: dt: 0.5000, sse=478604.6, rms=0.143 (0.000%)
- 025: dt: 0.5000, sse=477404.8, rms=0.143 (0.000%)
- 026: dt: 0.5000, sse=476307.0, rms=0.143 (0.000%)
- 027: dt: 0.5000, sse=475251.8, rms=0.143 (0.000%)
- 028: dt: 0.5000, sse=474003.1, rms=0.143 (0.000%)
- 029: dt: 0.5000, sse=472755.9, rms=0.144 (0.000%)
- 030: dt: 0.5000, sse=472009.8, rms=0.144 (0.000%)
- positioning took 4.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [102.80 231.20], gm=167.00+-21.40, and vertices in regions > 156.3
- 45313 surface locations found to contain inconsistent values (2095 in, 43218 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=49324.5, rms=0.13
- 031: dt: 0.5000, sse=49042.9, rms=0.124 (0.000%)
- 032: dt: 0.5000, sse=50265.4, rms=0.113 (0.000%)
- 033: dt: 0.5000, sse=51683.0, rms=0.105 (0.000%)
- 034: dt: 0.5000, sse=52895.4, rms=0.100 (0.000%)
- 035: dt: 0.5000, sse=53878.7, rms=0.095 (0.000%)
- 036: dt: 0.5000, sse=54822.2, rms=0.090 (0.000%)
- 037: dt: 0.5000, sse=55703.8, rms=0.085 (0.000%)
- 038: dt: 0.5000, sse=56564.3, rms=0.081 (0.000%)
- 039: dt: 0.5000, sse=57430.5, rms=0.077 (0.000%)
- 040: dt: 0.5000, sse=58277.3, rms=0.074 (0.000%)
- 041: dt: 0.5000, sse=59050.3, rms=0.071 (0.000%)
- 042: dt: 0.5000, sse=59801.1, rms=0.067 (0.000%)
- 043: dt: 0.5000, sse=60506.4, rms=0.065 (0.000%)
- 044: dt: 0.5000, sse=61189.5, rms=0.062 (0.000%)
- 045: dt: 0.5000, sse=61814.1, rms=0.060 (0.000%)
- 046: dt: 0.5000, sse=62407.8, rms=0.058 (0.000%)
- 047: dt: 0.5000, sse=62950.9, rms=0.055 (0.000%)
- 048: dt: 0.5000, sse=63444.4, rms=0.054 (0.000%)
- 049: dt: 0.5000, sse=63930.4, rms=0.052 (0.000%)
- 050: dt: 0.5000, sse=64379.0, rms=0.050 (0.000%)
- 051: dt: 0.5000, sse=64806.3, rms=0.049 (0.000%)
- 052: dt: 0.5000, sse=65179.3, rms=0.048 (0.000%)
- 053: dt: 0.5000, sse=65511.7, rms=0.046 (0.000%)
- 054: dt: 0.5000, sse=65844.9, rms=0.045 (0.000%)
- 055: dt: 0.5000, sse=66145.9, rms=0.044 (0.000%)
- 056: dt: 0.5000, sse=66411.4, rms=0.043 (0.000%)
- 057: dt: 0.5000, sse=66612.0, rms=0.042 (0.000%)
- 058: dt: 0.5000, sse=66851.4, rms=0.042 (0.000%)
- 059: dt: 0.5000, sse=67050.4, rms=0.041 (0.000%)
- 060: dt: 0.5000, sse=67243.6, rms=0.040 (0.000%)
- positioning took 5.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [63.40 268.60], gm=166.00+-34.20, and vertices in regions > 148.9
- 37661 surface locations found to contain inconsistent values (5 in, 37656 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=12155.9, rms=0.18
- 061: dt: 0.5000, sse=11530.2, rms=0.171 (0.000%)
- 062: dt: 0.5000, sse=10624.7, rms=0.153 (0.000%)
- 063: dt: 0.5000, sse=9952.6, rms=0.136 (0.000%)
- 064: dt: 0.5000, sse=9473.3, rms=0.121 (0.000%)
- 065: dt: 0.5000, sse=9178.2, rms=0.108 (0.000%)
- 066: dt: 0.5000, sse=9013.4, rms=0.098 (0.000%)
- 067: dt: 0.5000, sse=8920.9, rms=0.089 (0.000%)
- 068: dt: 0.5000, sse=8868.3, rms=0.083 (0.000%)
- 069: dt: 0.5000, sse=8861.6, rms=0.076 (0.000%)
- 070: dt: 0.5000, sse=8896.1, rms=0.071 (0.000%)
- 071: dt: 0.5000, sse=8960.4, rms=0.066 (0.000%)
- 072: dt: 0.5000, sse=9027.7, rms=0.062 (0.000%)
- 073: dt: 0.5000, sse=9092.5, rms=0.058 (0.000%)
- 074: dt: 0.5000, sse=9157.8, rms=0.054 (0.000%)
- 075: dt: 0.5000, sse=9223.9, rms=0.051 (0.000%)
- 076: dt: 0.5000, sse=9287.0, rms=0.048 (0.000%)
- 077: dt: 0.5000, sse=9349.0, rms=0.046 (0.000%)
- 078: dt: 0.5000, sse=9409.1, rms=0.044 (0.000%)
- 079: dt: 0.5000, sse=9464.9, rms=0.042 (0.000%)
- 080: dt: 0.5000, sse=9518.9, rms=0.040 (0.000%)
- 081: dt: 0.5000, sse=9571.4, rms=0.038 (0.000%)
- 082: dt: 0.5000, sse=9617.6, rms=0.037 (0.000%)
- 083: dt: 0.5000, sse=9662.5, rms=0.036 (0.000%)
- 084: dt: 0.5000, sse=9702.4, rms=0.035 (0.000%)
- 085: dt: 0.5000, sse=9738.6, rms=0.034 (0.000%)
- 086: dt: 0.5000, sse=9772.5, rms=0.033 (0.000%)
- 087: dt: 0.5000, sse=9803.9, rms=0.032 (0.000%)
- 088: dt: 0.5000, sse=9831.5, rms=0.032 (0.000%)
- 089: dt: 0.5000, sse=9856.0, rms=0.031 (0.000%)
- 090: dt: 0.5000, sse=9878.5, rms=0.031 (0.000%)
- positioning took 4.7 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [71.20 260.80], gm=166.00+-31.60, and vertices in regions > 150.2
- 10453 surface locations found to contain inconsistent values (10 in, 10443 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/sub006/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1900.5, rms=0.07
- 091: dt: 0.5000, sse=1866.7, rms=0.073 (0.000%)
- 092: dt: 0.5000, sse=1715.0, rms=0.067 (0.000%)
- 093: dt: 0.5000, sse=1589.9, rms=0.061 (0.000%)
- 094: dt: 0.5000, sse=1487.0, rms=0.056 (0.000%)
- 095: dt: 0.5000, sse=1408.0, rms=0.051 (0.000%)
- 096: dt: 0.5000, sse=1353.5, rms=0.048 (0.000%)
- 097: dt: 0.5000, sse=1316.5, rms=0.045 (0.000%)
- 098: dt: 0.5000, sse=1289.3, rms=0.043 (0.000%)
- 099: dt: 0.5000, sse=1264.8, rms=0.041 (0.000%)
- 100: dt: 0.5000, sse=1240.9, rms=0.039 (0.000%)
- 101: dt: 0.5000, sse=1219.6, rms=0.037 (0.000%)
- 102: dt: 0.5000, sse=1202.6, rms=0.035 (0.000%)
- 103: dt: 0.5000, sse=1188.9, rms=0.034 (0.000%)
- 104: dt: 0.5000, sse=1178.0, rms=0.033 (0.000%)
- 105: dt: 0.5000, sse=1169.0, rms=0.031 (0.000%)
- 106: dt: 0.5000, sse=1161.6, rms=0.030 (0.000%)
- 107: dt: 0.5000, sse=1155.5, rms=0.030 (0.000%)
- 108: dt: 0.5000, sse=1150.6, rms=0.029 (0.000%)
- 109: dt: 0.5000, sse=1147.0, rms=0.028 (0.000%)
- 110: dt: 0.5000, sse=1144.2, rms=0.028 (0.000%)
- 111: dt: 0.5000, sse=1141.2, rms=0.027 (0.000%)
- 112: dt: 0.5000, sse=1139.7, rms=0.027 (0.000%)
- 113: dt: 0.5000, sse=1138.0, rms=0.027 (0.000%)
- 114: dt: 0.5000, sse=1136.9, rms=0.026 (0.000%)
- 115: dt: 0.5000, sse=1135.8, rms=0.026 (0.000%)
- 116: dt: 0.5000, sse=1134.9, rms=0.026 (0.000%)
- 117: dt: 0.5000, sse=1134.2, rms=0.026 (0.000%)
- 118: dt: 0.5000, sse=1134.0, rms=0.026 (0.000%)
- 119: dt: 0.5000, sse=1133.7, rms=0.026 (0.000%)
- 120: dt: 0.5000, sse=1133.2, rms=0.026 (0.000%)
- positioning took 4.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.area.pial
- vertex spacing 1.04 +- 0.45 (0.06-->8.89) (max @ vno 77073 --> 73397)
- face area 0.42 +- 0.33 (0.00-->7.81)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 171478 vertices processed
- 25000 of 171478 vertices processed
- 50000 of 171478 vertices processed
- 75000 of 171478 vertices processed
- 100000 of 171478 vertices processed
- 125000 of 171478 vertices processed
- 150000 of 171478 vertices processed
- 0 of 171478 vertices processed
- 25000 of 171478 vertices processed
- 50000 of 171478 vertices processed
- 75000 of 171478 vertices processed
- 100000 of 171478 vertices processed
- 125000 of 171478 vertices processed
- 150000 of 171478 vertices processed
- thickness calculation complete, 260:847 truncations.
- 38131 vertices at 0 distance
- 119330 vertices at 1 distance
- 110616 vertices at 2 distance
- 44684 vertices at 3 distance
- 12417 vertices at 4 distance
- 3184 vertices at 5 distance
- 956 vertices at 6 distance
- 315 vertices at 7 distance
- 114 vertices at 8 distance
- 39 vertices at 9 distance
- 30 vertices at 10 distance
- 19 vertices at 11 distance
- 18 vertices at 12 distance
- 25 vertices at 13 distance
- 17 vertices at 14 distance
- 9 vertices at 15 distance
- 11 vertices at 16 distance
- 7 vertices at 17 distance
- 3 vertices at 18 distance
- 6 vertices at 19 distance
- 9 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.thickness
- positioning took 24.3 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub006 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/sub006/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- 25014 bright wm thresholded.
- 438 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig...
- computing class statistics...
- border white: 318128 voxels (1.90%)
- border gray 352780 voxels (2.10%)
- WM (93.0): 93.7 +- 10.3 [70.0 --> 110.0]
- GM (75.0) : 73.1 +- 13.4 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.6 (was 70)
- setting MAX_BORDER_WHITE to 116.3 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.2 (was 40)
- setting MAX_GRAY to 95.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=57
- mean inside = 93.6, mean outside = 67.7
- 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/sub006/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.03-->4.47) (max @ vno 43725 --> 169070)
- face area 0.33 +- 0.15 (0.00-->2.53)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- deleting segment 5 with 16 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- deleting segment 10 with 12 points - only 0.00% unknown
- deleting segment 11 with 355 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 14 with 11 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 15 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 16 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 17 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 18 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 19 with 1 points - only 0.00% unknown
- deleting segment 20 with 8 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 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070)
- face area 0.33 +- 0.15 (0.00-->2.53)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5232412.5, rms=0.00
- rms = 1.52, time step reduction 1 of 3 to 0.250...
- rms = 0.40, 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=5232412.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 16 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- deleting segment 9 with 355 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 11 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 14 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 16 with 1 points - only 0.00% unknown
- deleting segment 17 with 8 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 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070)
- face area 0.33 +- 0.15 (0.00-->2.53)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5232412.5, rms=0.00
- rms = 1.51, time step reduction 1 of 3 to 0.250...
- rms = 0.40, 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=5232412.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 16 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- deleting segment 9 with 355 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 11 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 14 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 16 with 1 points - only 0.00% unknown
- deleting segment 17 with 8 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 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070)
- face area 0.33 +- 0.15 (0.00-->2.53)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5232412.5, rms=0.00
- rms = 1.52, time step reduction 1 of 3 to 0.250...
- rms = 0.40, 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=5232412.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 16 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- deleting segment 9 with 355 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 11 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 14 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 16 with 1 points - only 0.00% unknown
- deleting segment 17 with 8 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=5232412.5, rms=0.00
- rms = 1.51, time step reduction 1 of 3 to 0.250...
- rms = 0.40, 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=5232412.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- 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 [120.90 215.10], gm=168.00+-15.70, and vertices in regions > 160.1
- 66741 surface locations found to contain inconsistent values (16077 in, 50664 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=583937.5, rms=0.31
- 001: dt: 0.5000, sse=551291.9, rms=0.299 (0.000%)
- 002: dt: 0.5000, sse=531946.6, rms=0.285 (0.000%)
- 003: dt: 0.5000, sse=521613.3, rms=0.273 (0.000%)
- 004: dt: 0.5000, sse=513313.1, rms=0.264 (0.000%)
- 005: dt: 0.5000, sse=507816.8, rms=0.255 (0.000%)
- 006: dt: 0.5000, sse=504162.0, rms=0.247 (0.000%)
- 007: dt: 0.5000, sse=502088.8, rms=0.240 (0.000%)
- 008: dt: 0.5000, sse=500069.7, rms=0.234 (0.000%)
- 009: dt: 0.5000, sse=498060.4, rms=0.228 (0.000%)
- 010: dt: 0.5000, sse=497946.9, rms=0.223 (0.000%)
- 011: dt: 0.5000, sse=496109.5, rms=0.218 (0.000%)
- 012: dt: 0.5000, sse=495622.3, rms=0.214 (0.000%)
- 013: dt: 0.5000, sse=494527.0, rms=0.210 (0.000%)
- 014: dt: 0.5000, sse=493889.6, rms=0.206 (0.000%)
- 015: dt: 0.5000, sse=492955.4, rms=0.203 (0.000%)
- 016: dt: 0.5000, sse=491788.3, rms=0.200 (0.000%)
- 017: dt: 0.5000, sse=491022.9, rms=0.197 (0.000%)
- 018: dt: 0.5000, sse=490132.5, rms=0.194 (0.000%)
- 019: dt: 0.5000, sse=489833.7, rms=0.191 (0.000%)
- 020: dt: 0.5000, sse=488871.8, rms=0.189 (0.000%)
- 021: dt: 0.5000, sse=487999.1, rms=0.187 (0.000%)
- 022: dt: 0.5000, sse=487343.7, rms=0.185 (0.000%)
- 023: dt: 0.5000, sse=486283.6, rms=0.183 (0.000%)
- 024: dt: 0.5000, sse=485447.2, rms=0.181 (0.000%)
- 025: dt: 0.5000, sse=484462.7, rms=0.179 (0.000%)
- 026: dt: 0.5000, sse=483647.3, rms=0.178 (0.000%)
- 027: dt: 0.5000, sse=483251.5, rms=0.176 (0.000%)
- 028: dt: 0.5000, sse=482651.1, rms=0.175 (0.000%)
- 029: dt: 0.5000, sse=481343.0, rms=0.174 (0.000%)
- 030: dt: 0.5000, sse=480459.8, rms=0.173 (0.000%)
- positioning took 5.0 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [76.30 255.70], gm=166.00+-29.90, and vertices in regions > 151.0
- 49970 surface locations found to contain inconsistent values (100 in, 49870 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=54304.9, rms=0.21
- 031: dt: 0.5000, sse=53312.4, rms=0.196 (0.000%)
- 032: dt: 0.5000, sse=52236.9, rms=0.177 (0.000%)
- 033: dt: 0.5000, sse=51999.8, rms=0.161 (0.000%)
- 034: dt: 0.5000, sse=52344.8, rms=0.147 (0.000%)
- 035: dt: 0.5000, sse=53118.3, rms=0.135 (0.000%)
- 036: dt: 0.5000, sse=53940.3, rms=0.125 (0.000%)
- 037: dt: 0.5000, sse=54820.1, rms=0.116 (0.000%)
- 038: dt: 0.5000, sse=55713.6, rms=0.108 (0.000%)
- 039: dt: 0.5000, sse=56747.7, rms=0.102 (0.000%)
- 040: dt: 0.5000, sse=57823.4, rms=0.096 (0.000%)
- 041: dt: 0.5000, sse=58912.9, rms=0.091 (0.000%)
- 042: dt: 0.5000, sse=60000.9, rms=0.086 (0.000%)
- 043: dt: 0.5000, sse=61020.5, rms=0.082 (0.000%)
- 044: dt: 0.5000, sse=61998.4, rms=0.078 (0.000%)
- 045: dt: 0.5000, sse=62877.1, rms=0.075 (0.000%)
- 046: dt: 0.5000, sse=63736.4, rms=0.072 (0.000%)
- 047: dt: 0.5000, sse=64541.3, rms=0.069 (0.000%)
- 048: dt: 0.5000, sse=65293.5, rms=0.066 (0.000%)
- 049: dt: 0.5000, sse=65989.3, rms=0.064 (0.000%)
- 050: dt: 0.5000, sse=66664.4, rms=0.062 (0.000%)
- 051: dt: 0.5000, sse=67276.1, rms=0.060 (0.000%)
- 052: dt: 0.5000, sse=67850.1, rms=0.058 (0.000%)
- 053: dt: 0.5000, sse=68409.1, rms=0.056 (0.000%)
- 054: dt: 0.5000, sse=68891.1, rms=0.054 (0.000%)
- 055: dt: 0.5000, sse=69357.8, rms=0.053 (0.000%)
- 056: dt: 0.5000, sse=69782.3, rms=0.051 (0.000%)
- 057: dt: 0.5000, sse=70202.2, rms=0.050 (0.000%)
- 058: dt: 0.5000, sse=70580.1, rms=0.049 (0.000%)
- 059: dt: 0.5000, sse=70922.8, rms=0.047 (0.000%)
- 060: dt: 0.5000, sse=71252.9, rms=0.046 (0.000%)
- positioning took 4.6 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [114.00 222.00], gm=168.00+-18.00, and vertices in regions > 159.0
- 37039 surface locations found to contain inconsistent values (15337 in, 21702 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=10268.8, rms=0.14
- 061: dt: 0.5000, sse=10068.2, rms=0.135 (0.000%)
- 062: dt: 0.5000, sse=9596.7, rms=0.125 (0.000%)
- 063: dt: 0.5000, sse=9328.5, rms=0.118 (0.000%)
- 064: dt: 0.5000, sse=9147.7, rms=0.111 (0.000%)
- 065: dt: 0.5000, sse=9011.6, rms=0.106 (0.000%)
- 066: dt: 0.5000, sse=8905.1, rms=0.101 (0.000%)
- 067: dt: 0.5000, sse=8808.3, rms=0.097 (0.000%)
- 068: dt: 0.5000, sse=8732.1, rms=0.093 (0.000%)
- 069: dt: 0.5000, sse=8673.0, rms=0.089 (0.000%)
- 070: dt: 0.5000, sse=8628.8, rms=0.085 (0.000%)
- 071: dt: 0.5000, sse=8600.9, rms=0.081 (0.000%)
- 072: dt: 0.5000, sse=8578.6, rms=0.077 (0.000%)
- 073: dt: 0.5000, sse=8558.2, rms=0.074 (0.000%)
- 074: dt: 0.5000, sse=8545.4, rms=0.071 (0.000%)
- 075: dt: 0.5000, sse=8538.6, rms=0.068 (0.000%)
- 076: dt: 0.5000, sse=8539.4, rms=0.065 (0.000%)
- 077: dt: 0.5000, sse=8544.7, rms=0.062 (0.000%)
- 078: dt: 0.5000, sse=8548.4, rms=0.060 (0.000%)
- 079: dt: 0.5000, sse=8557.6, rms=0.058 (0.000%)
- 080: dt: 0.5000, sse=8572.7, rms=0.055 (0.000%)
- 081: dt: 0.5000, sse=8582.5, rms=0.053 (0.000%)
- 082: dt: 0.5000, sse=8600.0, rms=0.051 (0.000%)
- 083: dt: 0.5000, sse=8613.9, rms=0.049 (0.000%)
- 084: dt: 0.5000, sse=8633.2, rms=0.048 (0.000%)
- 085: dt: 0.5000, sse=8649.9, rms=0.046 (0.000%)
- 086: dt: 0.5000, sse=8660.2, rms=0.045 (0.000%)
- 087: dt: 0.5000, sse=8676.0, rms=0.043 (0.000%)
- 088: dt: 0.5000, sse=8688.7, rms=0.042 (0.000%)
- 089: dt: 0.5000, sse=8703.5, rms=0.041 (0.000%)
- 090: dt: 0.5000, sse=8719.0, rms=0.040 (0.000%)
- positioning took 4.6 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [91.20 244.80], gm=168.00+-25.60, and vertices in regions > 155.2
- 13872 surface locations found to contain inconsistent values (48 in, 13824 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/sub006/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=2027.1, rms=0.09
- 091: dt: 0.5000, sse=1969.7, rms=0.083 (0.000%)
- 092: dt: 0.5000, sse=1765.6, rms=0.075 (0.000%)
- 093: dt: 0.5000, sse=1605.0, rms=0.068 (0.000%)
- 094: dt: 0.5000, sse=1477.9, rms=0.061 (0.000%)
- 095: dt: 0.5000, sse=1383.8, rms=0.056 (0.000%)
- 096: dt: 0.5000, sse=1322.9, rms=0.052 (0.000%)
- 097: dt: 0.5000, sse=1277.8, rms=0.049 (0.000%)
- 098: dt: 0.5000, sse=1243.1, rms=0.046 (0.000%)
- 099: dt: 0.5000, sse=1214.2, rms=0.044 (0.000%)
- 100: dt: 0.5000, sse=1186.9, rms=0.042 (0.000%)
- 101: dt: 0.5000, sse=1165.8, rms=0.040 (0.000%)
- 102: dt: 0.5000, sse=1148.6, rms=0.038 (0.000%)
- 103: dt: 0.5000, sse=1134.2, rms=0.036 (0.000%)
- 104: dt: 0.5000, sse=1122.8, rms=0.035 (0.000%)
- 105: dt: 0.5000, sse=1113.8, rms=0.034 (0.000%)
- 106: dt: 0.5000, sse=1107.0, rms=0.033 (0.000%)
- 107: dt: 0.5000, sse=1101.6, rms=0.032 (0.000%)
- 108: dt: 0.5000, sse=1096.5, rms=0.031 (0.000%)
- 109: dt: 0.5000, sse=1092.6, rms=0.031 (0.000%)
- 110: dt: 0.5000, sse=1089.5, rms=0.030 (0.000%)
- 111: dt: 0.5000, sse=1087.5, rms=0.030 (0.000%)
- 112: dt: 0.5000, sse=1084.6, rms=0.030 (0.000%)
- 113: dt: 0.5000, sse=1082.9, rms=0.029 (0.000%)
- 114: dt: 0.5000, sse=1081.3, rms=0.029 (0.000%)
- 115: dt: 0.5000, sse=1079.9, rms=0.029 (0.000%)
- 116: dt: 0.5000, sse=1079.9, rms=0.029 (0.000%)
- 117: dt: 0.5000, sse=1079.1, rms=0.029 (0.000%)
- 118: dt: 0.5000, sse=1079.3, rms=0.028 (0.000%)
- 119: dt: 0.5000, sse=1078.9, rms=0.028 (0.000%)
- 120: dt: 0.5000, sse=1078.6, rms=0.028 (0.000%)
- positioning took 4.6 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.area.pial
- vertex spacing 1.04 +- 0.45 (0.09-->8.56) (max @ vno 120578 --> 119429)
- face area 0.42 +- 0.32 (0.00-->9.00)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 169645 vertices processed
- 25000 of 169645 vertices processed
- 50000 of 169645 vertices processed
- 75000 of 169645 vertices processed
- 100000 of 169645 vertices processed
- 125000 of 169645 vertices processed
- 150000 of 169645 vertices processed
- 0 of 169645 vertices processed
- 25000 of 169645 vertices processed
- 50000 of 169645 vertices processed
- 75000 of 169645 vertices processed
- 100000 of 169645 vertices processed
- 125000 of 169645 vertices processed
- 150000 of 169645 vertices processed
- thickness calculation complete, 257:851 truncations.
- 39532 vertices at 0 distance
- 119234 vertices at 1 distance
- 109115 vertices at 2 distance
- 42502 vertices at 3 distance
- 11691 vertices at 4 distance
- 2940 vertices at 5 distance
- 812 vertices at 6 distance
- 270 vertices at 7 distance
- 102 vertices at 8 distance
- 56 vertices at 9 distance
- 41 vertices at 10 distance
- 34 vertices at 11 distance
- 23 vertices at 12 distance
- 18 vertices at 13 distance
- 13 vertices at 14 distance
- 12 vertices at 15 distance
- 11 vertices at 16 distance
- 10 vertices at 17 distance
- 12 vertices at 18 distance
- 6 vertices at 19 distance
- 10 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.thickness
- positioning took 23.5 minutes
- #--------------------------------------------
- #@# Surf Volume lh Fri Aug 9 00:23:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Fri Aug 9 00:23:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Fri Aug 9 00:23:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub006
- 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 = 10
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Fri Aug 9 00:58:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006
- 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 sub006
- $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 sub006
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1428534 mm^3 (det: 1.363710 )
- Computing euler number
- orig.nofix lheno = -30, rheno = -44
- orig.nofix lhholes = 16, rhholes = 23
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 336212.563 332461.000 diff= 3751.6 pctdiff= 1.116
- rhCtxGM: 328476.300 325187.000 diff= 3289.3 pctdiff= 1.001
- lhCtxWM: 277850.585 277588.500 diff= 262.1 pctdiff= 0.094
- rhCtxWM: 278985.206 278975.500 diff= 9.7 pctdiff= 0.003
- SubCortGMVol 73421.000
- SupraTentVol 1315795.655 (1307464.000) diff=8331.655 pctdiff=0.633
- SupraTentVolNotVent 1296172.655 (1287841.000) diff=8331.655 pctdiff=0.643
- BrainSegVol 1456908.000 (1453971.000) diff=2937.000 pctdiff=0.202
- BrainSegVolNotVent 1433208.000 (1440132.655) diff=-6924.655 pctdiff=-0.483
- BrainSegVolNotVent 1433208.000
- CerebellumVol 144979.000
- VentChorVol 19623.000
- 3rd4th5thCSF 4077.000
- CSFVol 1172.000, OptChiasmVol 356.000
- MaskVol 1955327.000
- 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 7330 7330.012
- 4 5 Left-Inf-Lat-Vent 485 485.404
- 5 7 Left-Cerebellum-White-Matter 19126 19126.078
- 6 8 Left-Cerebellum-Cortex 54076 54075.738
- 7 10 Left-Thalamus-Proper 9801 9800.789
- 8 11 Left-Caudate 4593 4592.850
- 9 12 Left-Putamen 6882 6882.185
- 10 13 Left-Pallidum 2582 2581.743
- 11 14 3rd-Ventricle 1031 1030.534
- 12 15 4th-Ventricle 2076 2076.042
- 13 16 Brain-Stem 28015 28015.285
- 14 17 Left-Hippocampus 4356 4355.679
- 15 18 Left-Amygdala 1830 1830.003
- 16 24 CSF 1168 1167.957
- 17 26 Left-Accumbens-area 1138 1137.688
- 18 28 Left-VentralDC 4830 4829.687
- 19 30 Left-vessel 89 88.732
- 20 31 Left-choroid-plexus 1089 1088.721
- 23 43 Right-Lateral-Ventricle 8169 8168.733
- 24 44 Right-Inf-Lat-Vent 835 834.640
- 25 46 Right-Cerebellum-White-Matter 19688 19687.779
- 26 47 Right-Cerebellum-Cortex 54426 54426.105
- 27 49 Right-Thalamus-Proper 8898 8898.092
- 28 50 Right-Caudate 5030 5030.434
- 29 51 Right-Putamen 6987 6987.416
- 30 52 Right-Pallidum 2747 2746.605
- 31 53 Right-Hippocampus 4251 4250.944
- 32 54 Right-Amygdala 1875 1875.328
- 33 58 Right-Accumbens-area 902 901.986
- 34 60 Right-VentralDC 4849 4848.833
- 35 62 Right-vessel 98 97.882
- 36 63 Right-choroid-plexus 1666 1665.774
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 1291 1290.874
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 30 29.574
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 360 359.910
- 45 251 CC_Posterior 733 732.649
- 46 252 CC_Mid_Posterior 381 380.823
- 47 253 CC_Central 374 373.556
- 48 254 CC_Mid_Anterior 392 392.228
- 49 255 CC_Anterior 867 866.925
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Fri Aug 9 01:02:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006
- mri_aparc2aseg --s sub006 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub006
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/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/sub006/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 = 655708
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006
- mri_aparc2aseg --s sub006 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub006
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/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/sub006/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 = 655708
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Fri Aug 9 01:08:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006
- mri_aparc2aseg --s sub006 --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 sub006
- 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/sub006/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 9139 vertices from left hemi
- Ripped 8689 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/sub006/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 1211345
- Used brute-force search on 255 voxels
- Fixing Parahip LH WM
- Found 14 clusters
- 0 k 7.000000
- 1 k 2.000000
- 2 k 1.000000
- 3 k 2.000000
- 4 k 3.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 1.000000
- 8 k 1.000000
- 9 k 1.000000
- 10 k 1.000000
- 11 k 1683.000000
- 12 k 36.000000
- 13 k 2.000000
- Fixing Parahip RH WM
- Found 4 clusters
- 0 k 1757.000000
- 1 k 1.000000
- 2 k 8.000000
- 3 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006
- 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 sub006 --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 sub006 --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) = 1428534 mm^3 (det: 1.363710 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 336212.563 332461.000 diff= 3751.6 pctdiff= 1.116
- rhCtxGM: 328476.300 325187.000 diff= 3289.3 pctdiff= 1.001
- lhCtxWM: 277850.585 277588.500 diff= 262.1 pctdiff= 0.094
- rhCtxWM: 278985.206 278975.500 diff= 9.7 pctdiff= 0.003
- SubCortGMVol 73421.000
- SupraTentVol 1315795.655 (1307464.000) diff=8331.655 pctdiff=0.633
- SupraTentVolNotVent 1296172.655 (1287841.000) diff=8331.655 pctdiff=0.643
- BrainSegVol 1456908.000 (1453971.000) diff=2937.000 pctdiff=0.202
- BrainSegVolNotVent 1433208.000 (1440132.655) diff=-6924.655 pctdiff=-0.483
- BrainSegVolNotVent 1433208.000
- CerebellumVol 144979.000
- VentChorVol 19623.000
- 3rd4th5thCSF 4077.000
- CSFVol 1172.000, OptChiasmVol 356.000
- MaskVol 1955327.000
- 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 4418 4417.723
- 2 3002 wm-lh-caudalanteriorcingulate 3864 3864.340
- 3 3003 wm-lh-caudalmiddlefrontal 7755 7755.121
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2922 2922.244
- 6 3006 wm-lh-entorhinal 866 865.680
- 7 3007 wm-lh-fusiform 7879 7879.229
- 8 3008 wm-lh-inferiorparietal 13874 13874.421
- 9 3009 wm-lh-inferiortemporal 8577 8576.690
- 10 3010 wm-lh-isthmuscingulate 5079 5079.076
- 11 3011 wm-lh-lateraloccipital 11434 11433.657
- 12 3012 wm-lh-lateralorbitofrontal 7590 7590.018
- 13 3013 wm-lh-lingual 5167 5166.894
- 14 3014 wm-lh-medialorbitofrontal 4050 4049.541
- 15 3015 wm-lh-middletemporal 6849 6848.841
- 16 3016 wm-lh-parahippocampal 1745 1745.474
- 17 3017 wm-lh-paracentral 4994 4993.876
- 18 3018 wm-lh-parsopercularis 5347 5347.052
- 19 3019 wm-lh-parsorbitalis 1058 1058.097
- 20 3020 wm-lh-parstriangularis 3877 3876.976
- 21 3021 wm-lh-pericalcarine 3776 3775.736
- 22 3022 wm-lh-postcentral 9375 9375.486
- 23 3023 wm-lh-posteriorcingulate 5697 5696.546
- 24 3024 wm-lh-precentral 15315 15314.828
- 25 3025 wm-lh-precuneus 12411 12410.523
- 26 3026 wm-lh-rostralanteriorcingulate 3254 3253.774
- 27 3027 wm-lh-rostralmiddlefrontal 14948 14948.436
- 28 3028 wm-lh-superiorfrontal 24509 24508.672
- 29 3029 wm-lh-superiorparietal 14397 14396.718
- 30 3030 wm-lh-superiortemporal 8630 8630.139
- 31 3031 wm-lh-supramarginal 12144 12143.636
- 32 3032 wm-lh-frontalpole 242 241.895
- 33 3033 wm-lh-temporalpole 663 662.969
- 34 3034 wm-lh-transversetemporal 896 895.882
- 35 3035 wm-lh-insula 11996 11995.933
- 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 3372 3371.896
- 120 4002 wm-rh-caudalanteriorcingulate 3721 3721.009
- 121 4003 wm-rh-caudalmiddlefrontal 7093 7092.917
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2876 2875.500
- 124 4006 wm-rh-entorhinal 742 741.779
- 125 4007 wm-rh-fusiform 8916 8916.202
- 126 4008 wm-rh-inferiorparietal 16859 16858.648
- 127 4009 wm-rh-inferiortemporal 6662 6662.298
- 128 4010 wm-rh-isthmuscingulate 3680 3679.761
- 129 4011 wm-rh-lateraloccipital 11668 11668.020
- 130 4012 wm-rh-lateralorbitofrontal 8058 8058.475
- 131 4013 wm-rh-lingual 5615 5615.262
- 132 4014 wm-rh-medialorbitofrontal 4398 4398.331
- 133 4015 wm-rh-middletemporal 7127 7127.338
- 134 4016 wm-rh-parahippocampal 1785 1785.232
- 135 4017 wm-rh-paracentral 7082 7082.070
- 136 4018 wm-rh-parsopercularis 3396 3396.415
- 137 4019 wm-rh-parsorbitalis 1044 1044.153
- 138 4020 wm-rh-parstriangularis 4546 4545.789
- 139 4021 wm-rh-pericalcarine 4072 4071.632
- 140 4022 wm-rh-postcentral 9982 9982.438
- 141 4023 wm-rh-posteriorcingulate 5548 5548.213
- 142 4024 wm-rh-precentral 17896 17895.854
- 143 4025 wm-rh-precuneus 12276 12276.496
- 144 4026 wm-rh-rostralanteriorcingulate 2472 2471.522
- 145 4027 wm-rh-rostralmiddlefrontal 17153 17153.137
- 146 4028 wm-rh-superiorfrontal 22915 22914.824
- 147 4029 wm-rh-superiorparietal 13379 13379.062
- 148 4030 wm-rh-superiortemporal 8384 8383.724
- 149 4031 wm-rh-supramarginal 10440 10439.874
- 150 4032 wm-rh-frontalpole 371 370.807
- 151 4033 wm-rh-temporalpole 824 823.720
- 152 4034 wm-rh-transversetemporal 747 746.819
- 153 4035 wm-rh-insula 10663 10662.812
- 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 35030 35030.414
- 237 5002 Right-UnsegmentedWhiteMatter 35614 35613.559
- 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/sub006/label
- #--------------------------------------------
- #@# BA Labels lh Fri Aug 9 01:20:29 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 550
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4679
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 965
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8874
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 323
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4400
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 716
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6699
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 915
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6699
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 541
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4611
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 3216
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 16805
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 1125
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 5306
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 1858
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 5280
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 1794
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6435
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 3925
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 12039
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 721
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2739
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 133
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1332
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 194
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1208
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 273
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2365
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 63
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1567
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 338
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2334
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 414
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2733
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 203
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1752
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 1544
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 8579
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 610
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2522
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 787
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1938
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 1254
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4659
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 1742
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 5076
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
- Number of reverse mapping hits = 105
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 618
- mri_label2label: Done
- mris_label2annot --s sub006 --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/sub006/label
- cmdline mris_label2annot --s sub006 --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 sub006
- 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/sub006/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 119564 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.BA.annot
- mris_label2annot --s sub006 --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/sub006/label
- cmdline mris_label2annot --s sub006 --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 sub006
- 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/sub006/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 141481 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub006 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 1378 807 3306 2.741 0.426 0.156 0.056 31 2.8 BA1
- 4430 2985 8490 2.575 0.472 0.126 0.036 51 6.3 BA2
- 1063 731 1176 2.100 0.429 0.124 0.032 7 1.4 BA3a
- 2986 1952 4892 2.120 0.531 0.115 0.030 33 3.7 BA3b
- 2212 1327 5542 3.143 0.534 0.108 0.037 33 3.8 BA4a
- 1633 990 3294 3.204 0.511 0.087 0.028 10 2.2 BA4p
- 12933 8663 33247 2.976 0.590 0.127 0.036 155 19.9 BA6
- 3462 2296 7744 2.848 0.477 0.131 0.040 50 5.7 BA44
- 4517 2998 9386 2.593 0.519 0.150 0.052 81 9.7 BA45
- 4068 2705 6033 2.041 0.453 0.143 0.060 70 9.9 V1
- 9771 6406 15502 2.210 0.529 0.161 0.069 215 26.7 V2
- 2425 1628 4352 2.448 0.436 0.141 0.044 34 4.1 MT
- 1036 740 3633 3.547 0.666 0.143 0.047 15 2.2 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub006 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 916 498 2199 2.777 0.451 0.161 0.063 24 2.2 BA1
- 1751 1201 3672 2.621 0.441 0.118 0.029 18 2.0 BA2
- 888 608 917 2.063 0.437 0.127 0.032 6 1.3 BA3a
- 1918 1249 2800 1.992 0.439 0.095 0.021 13 1.6 BA3b
- 2123 1298 5281 3.195 0.550 0.096 0.024 18 2.4 BA4a
- 1272 785 2439 3.106 0.523 0.090 0.027 9 1.4 BA4p
- 7237 4829 18409 2.940 0.595 0.124 0.034 86 10.7 BA6
- 2322 1552 5408 2.887 0.475 0.137 0.042 35 3.9 BA44
- 1901 1245 4596 2.785 0.482 0.168 0.066 48 5.2 BA45
- 4307 2867 6459 2.040 0.454 0.144 0.061 78 10.5 V1
- 4819 3198 6972 2.041 0.499 0.172 0.078 116 14.3 V2
- 543 373 907 2.204 0.405 0.120 0.027 5 0.6 MT
- #--------------------------------------------
- #@# BA Labels rh Fri Aug 9 01:25:46 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 497
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4459
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 818
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 7505
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 367
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4347
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 564
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 5086
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 1117
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 6864
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 565
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 5038
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 2990
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 15246
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 1139
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 8051
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 1562
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6917
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 2392
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 7119
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 4535
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 12551
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 1008
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2940
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 79
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 831
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 160
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 1036
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 317
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 3005
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 98
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1796
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 332
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2515
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 177
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1565
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 218
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1707
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 1884
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 8843
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 161
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1173
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 215
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1393
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 1582
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4814
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 1924
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 5361
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub006 --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 = sub006
- 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/sub006/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
- Number of reverse mapping hits = 157
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 425
- mri_label2label: Done
- mris_label2annot --s sub006 --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/sub006/label
- cmdline mris_label2annot --s sub006 --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 sub006
- 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/sub006/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 118049 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.BA.annot
- mris_label2annot --s sub006 --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/sub006/label
- cmdline mris_label2annot --s sub006 --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 sub006
- 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/sub006/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 141116 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub006 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 1105 660 2688 2.770 0.422 0.143 0.040 17 1.9 BA1
- 3922 2579 6929 2.511 0.470 0.110 0.028 34 4.6 BA2
- 1273 831 1327 2.040 0.505 0.122 0.035 10 1.8 BA3a
- 2457 1582 3835 2.036 0.491 0.112 0.036 23 4.3 BA3b
- 2087 1284 4635 2.870 0.719 0.107 0.029 18 2.8 BA4a
- 1453 941 2898 2.968 0.584 0.105 0.030 9 1.9 BA4p
- 11589 7829 29107 2.978 0.623 0.125 0.035 133 16.2 BA6
- 4073 2738 8712 2.858 0.456 0.123 0.032 43 5.7 BA44
- 5202 3488 11692 2.693 0.482 0.145 0.051 92 10.0 BA45
- 4782 3197 7009 2.051 0.442 0.146 0.059 93 12.0 V1
- 10170 6679 16461 2.231 0.498 0.155 0.063 177 21.8 V2
- 2839 1860 4901 2.463 0.467 0.135 0.040 41 4.5 MT
- 644 476 1946 3.377 0.629 0.144 0.047 7 1.3 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub006 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 789 452 1909 2.817 0.358 0.137 0.041 12 1.2 BA1
- 2254 1479 4014 2.489 0.475 0.103 0.024 16 2.4 BA2
- 1075 699 1063 2.043 0.493 0.123 0.036 7 1.6 BA3a
- 2021 1352 2836 1.912 0.421 0.102 0.024 14 2.1 BA3b
- 1150 712 2500 2.590 0.737 0.118 0.033 12 1.4 BA4a
- 1226 784 2518 3.157 0.527 0.104 0.030 8 1.6 BA4p
- 7764 5223 18944 2.911 0.643 0.125 0.035 91 10.9 BA6
- 954 667 2456 2.956 0.493 0.135 0.038 13 1.6 BA44
- 1186 821 3175 2.892 0.374 0.142 0.049 21 2.2 BA45
- 4570 3064 6629 2.052 0.441 0.143 0.057 84 11.5 V1
- 5134 3415 7778 2.088 0.498 0.171 0.075 100 12.6 V2
- 406 245 837 2.678 0.306 0.149 0.048 8 0.8 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 01:31:00 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub006 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub006.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1003 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub006 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 368 242 1509 3.742 0.513 0.126 0.051 5 0.9 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 01:31:17 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub006 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub006.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 789 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub006 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
- 283 193 947 3.346 0.579 0.139 0.039 3 0.5 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:53:55 CEST 2013
- Ended at Fri Aug 9 01:31:34 CEST 2013
- #@#%# recon-all-run-time-hours 14.627
- recon-all -s sub006 finished without error at Fri Aug 9 01:31:34 CEST 2013
|