| 12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485868788899091929394959697989910010110210310410510610710810911011111211311411511611711811912012112212312412512612712812913013113213313413513613713813914014114214314414514614714814915015115215315415515615715815916016116216316416516616716816917017117217317417517617717817918018118218318418518618718818919019119219319419519619719819920020120220320420520620720820921021121221321421521621721821922022122222322422522622722822923023123223323423523623723823924024124224324424524624724824925025125225325425525625725825926026126226326426526626726826927027127227327427527627727827928028128228328428528628728828929029129229329429529629729829930030130230330430530630730830931031131231331431531631731831932032132232332432532632732832933033133233333433533633733833934034134234334434534634734834935035135235335435535635735835936036136236336436536636736836937037137237337437537637737837938038138238338438538638738838939039139239339439539639739839940040140240340440540640740840941041141241341441541641741841942042142242342442542642742842943043143243343443543643743843944044144244344444544644744844945045145245345445545645745845946046146246346446546646746846947047147247347447547647747847948048148248348448548648748848949049149249349449549649749849950050150250350450550650750850951051151251351451551651751851952052152252352452552652752852953053153253353453553653753853954054154254354454554654754854955055155255355455555655755855956056156256356456556656756856957057157257357457557657757857958058158258358458558658758858959059159259359459559659759859960060160260360460560660760860961061161261361461561661761861962062162262362462562662762862963063163263363463563663763863964064164264364464564664764864965065165265365465565665765865966066166266366466566666766866967067167267367467567667767867968068168268368468568668768868969069169269369469569669769869970070170270370470570670770870971071171271371471571671771871972072172272372472572672772872973073173273373473573673773873974074174274374474574674774874975075175275375475575675775875976076176276376476576676776876977077177277377477577677777877978078178278378478578678778878979079179279379479579679779879980080180280380480580680780880981081181281381481581681781881982082182282382482582682782882983083183283383483583683783883984084184284384484584684784884985085185285385485585685785885986086186286386486586686786886987087187287387487587687787887988088188288388488588688788888989089189289389489589689789889990090190290390490590690790890991091191291391491591691791891992092192292392492592692792892993093193293393493593693793893994094194294394494594694794894995095195295395495595695795895996096196296396496596696796896997097197297397497597697797897998098198298398498598698798898999099199299399499599699799899910001001100210031004100510061007100810091010101110121013101410151016101710181019102010211022102310241025102610271028102910301031103210331034103510361037103810391040104110421043104410451046104710481049105010511052105310541055105610571058105910601061106210631064106510661067106810691070107110721073107410751076107710781079108010811082108310841085108610871088108910901091109210931094109510961097109810991100110111021103110411051106110711081109111011111112111311141115111611171118111911201121112211231124112511261127112811291130113111321133113411351136113711381139114011411142114311441145114611471148114911501151115211531154115511561157115811591160116111621163116411651166116711681169117011711172117311741175117611771178117911801181118211831184118511861187118811891190119111921193119411951196119711981199120012011202120312041205120612071208120912101211121212131214121512161217121812191220122112221223122412251226122712281229123012311232123312341235123612371238123912401241124212431244124512461247124812491250125112521253125412551256125712581259126012611262126312641265126612671268126912701271127212731274127512761277127812791280128112821283128412851286128712881289129012911292129312941295129612971298129913001301130213031304130513061307130813091310131113121313131413151316131713181319132013211322132313241325132613271328132913301331133213331334133513361337133813391340134113421343134413451346134713481349135013511352135313541355135613571358135913601361136213631364136513661367136813691370137113721373137413751376137713781379138013811382138313841385138613871388138913901391139213931394139513961397139813991400140114021403140414051406140714081409141014111412141314141415141614171418141914201421142214231424142514261427142814291430143114321433143414351436143714381439144014411442144314441445144614471448144914501451145214531454145514561457145814591460146114621463146414651466146714681469147014711472147314741475147614771478147914801481148214831484148514861487148814891490149114921493149414951496149714981499150015011502150315041505150615071508150915101511151215131514151515161517151815191520152115221523152415251526152715281529153015311532153315341535153615371538153915401541154215431544154515461547154815491550155115521553155415551556155715581559156015611562156315641565156615671568156915701571157215731574157515761577157815791580158115821583158415851586158715881589159015911592159315941595159615971598159916001601160216031604160516061607160816091610161116121613161416151616161716181619162016211622162316241625162616271628162916301631163216331634163516361637163816391640164116421643164416451646164716481649165016511652165316541655165616571658165916601661166216631664166516661667166816691670167116721673167416751676167716781679168016811682168316841685168616871688168916901691169216931694169516961697169816991700170117021703170417051706170717081709171017111712171317141715171617171718171917201721172217231724172517261727172817291730173117321733173417351736173717381739174017411742174317441745174617471748174917501751175217531754175517561757175817591760176117621763176417651766176717681769177017711772177317741775177617771778177917801781178217831784178517861787178817891790179117921793179417951796179717981799180018011802180318041805180618071808180918101811181218131814181518161817181818191820182118221823182418251826182718281829183018311832183318341835183618371838183918401841184218431844184518461847184818491850185118521853185418551856185718581859186018611862186318641865186618671868186918701871187218731874187518761877187818791880188118821883188418851886188718881889189018911892189318941895189618971898189919001901190219031904190519061907190819091910191119121913191419151916191719181919192019211922192319241925192619271928192919301931193219331934193519361937193819391940194119421943194419451946194719481949195019511952195319541955195619571958195919601961196219631964196519661967196819691970197119721973197419751976197719781979198019811982198319841985198619871988198919901991199219931994199519961997199819992000200120022003200420052006200720082009201020112012201320142015201620172018201920202021202220232024202520262027202820292030203120322033203420352036203720382039204020412042204320442045204620472048204920502051205220532054205520562057205820592060206120622063206420652066206720682069207020712072207320742075207620772078207920802081208220832084208520862087208820892090209120922093209420952096209720982099210021012102210321042105210621072108210921102111211221132114211521162117211821192120212121222123212421252126212721282129213021312132213321342135213621372138213921402141214221432144214521462147214821492150215121522153215421552156215721582159216021612162216321642165216621672168216921702171217221732174217521762177217821792180218121822183218421852186218721882189219021912192219321942195219621972198219922002201220222032204220522062207220822092210221122122213221422152216221722182219222022212222222322242225222622272228222922302231223222332234223522362237223822392240224122422243224422452246224722482249225022512252225322542255225622572258225922602261226222632264226522662267226822692270227122722273227422752276227722782279228022812282228322842285228622872288228922902291229222932294229522962297229822992300230123022303230423052306230723082309231023112312231323142315231623172318231923202321232223232324232523262327232823292330233123322333233423352336233723382339234023412342234323442345234623472348234923502351235223532354235523562357235823592360236123622363236423652366236723682369237023712372237323742375237623772378237923802381238223832384238523862387238823892390239123922393239423952396239723982399240024012402240324042405240624072408240924102411241224132414241524162417241824192420242124222423242424252426242724282429243024312432243324342435243624372438243924402441244224432444244524462447244824492450245124522453245424552456245724582459246024612462246324642465246624672468246924702471247224732474247524762477247824792480248124822483248424852486248724882489249024912492249324942495249624972498249925002501250225032504250525062507250825092510251125122513251425152516251725182519252025212522252325242525252625272528252925302531253225332534253525362537253825392540254125422543254425452546254725482549255025512552255325542555255625572558255925602561256225632564256525662567256825692570257125722573257425752576257725782579258025812582258325842585258625872588258925902591259225932594259525962597259825992600260126022603260426052606260726082609261026112612261326142615261626172618261926202621262226232624262526262627262826292630263126322633263426352636263726382639264026412642264326442645264626472648264926502651265226532654265526562657265826592660266126622663266426652666266726682669267026712672267326742675267626772678267926802681268226832684268526862687268826892690269126922693269426952696269726982699270027012702270327042705270627072708270927102711271227132714271527162717271827192720272127222723272427252726272727282729273027312732273327342735273627372738273927402741274227432744274527462747274827492750275127522753275427552756275727582759276027612762276327642765276627672768276927702771277227732774277527762777277827792780278127822783278427852786278727882789279027912792279327942795279627972798279928002801280228032804280528062807280828092810281128122813281428152816281728182819282028212822282328242825282628272828282928302831283228332834283528362837283828392840284128422843284428452846284728482849285028512852285328542855285628572858285928602861286228632864286528662867286828692870287128722873287428752876287728782879288028812882288328842885288628872888288928902891289228932894289528962897289828992900290129022903290429052906290729082909291029112912291329142915291629172918291929202921292229232924292529262927292829292930293129322933293429352936293729382939294029412942294329442945294629472948294929502951295229532954295529562957295829592960296129622963296429652966296729682969297029712972297329742975297629772978297929802981298229832984298529862987298829892990299129922993299429952996299729982999300030013002300330043005300630073008300930103011301230133014301530163017301830193020302130223023302430253026302730283029303030313032303330343035303630373038303930403041304230433044304530463047304830493050305130523053305430553056305730583059306030613062306330643065306630673068306930703071307230733074307530763077307830793080308130823083308430853086308730883089309030913092309330943095309630973098309931003101310231033104310531063107310831093110311131123113311431153116311731183119312031213122312331243125312631273128312931303131313231333134313531363137313831393140314131423143314431453146314731483149315031513152315331543155315631573158315931603161316231633164316531663167316831693170317131723173317431753176317731783179318031813182318331843185318631873188318931903191319231933194319531963197319831993200320132023203320432053206320732083209321032113212321332143215321632173218321932203221322232233224322532263227322832293230323132323233323432353236323732383239324032413242324332443245324632473248324932503251325232533254325532563257325832593260326132623263326432653266326732683269327032713272327332743275327632773278327932803281328232833284328532863287328832893290329132923293329432953296329732983299330033013302330333043305330633073308330933103311331233133314331533163317331833193320332133223323332433253326332733283329333033313332333333343335333633373338333933403341334233433344334533463347334833493350335133523353335433553356335733583359336033613362336333643365336633673368336933703371337233733374337533763377337833793380338133823383338433853386338733883389339033913392339333943395339633973398339934003401340234033404340534063407340834093410341134123413341434153416341734183419342034213422342334243425342634273428342934303431343234333434343534363437343834393440344134423443344434453446344734483449345034513452345334543455345634573458345934603461346234633464346534663467346834693470347134723473347434753476347734783479348034813482348334843485348634873488348934903491349234933494349534963497349834993500350135023503350435053506350735083509351035113512351335143515351635173518351935203521352235233524352535263527352835293530353135323533353435353536353735383539354035413542354335443545354635473548354935503551355235533554355535563557355835593560356135623563356435653566356735683569357035713572357335743575357635773578357935803581358235833584358535863587358835893590359135923593359435953596359735983599360036013602360336043605360636073608360936103611361236133614361536163617361836193620362136223623362436253626362736283629363036313632363336343635363636373638363936403641364236433644364536463647364836493650365136523653365436553656365736583659366036613662366336643665366636673668366936703671367236733674367536763677367836793680368136823683368436853686368736883689369036913692369336943695369636973698369937003701370237033704370537063707370837093710371137123713371437153716371737183719372037213722372337243725372637273728372937303731373237333734373537363737373837393740374137423743374437453746374737483749375037513752375337543755375637573758375937603761376237633764376537663767376837693770377137723773377437753776377737783779378037813782378337843785378637873788378937903791379237933794379537963797379837993800380138023803380438053806380738083809381038113812381338143815381638173818381938203821382238233824382538263827382838293830383138323833383438353836383738383839384038413842384338443845384638473848384938503851385238533854385538563857385838593860386138623863386438653866386738683869387038713872387338743875387638773878387938803881388238833884388538863887388838893890389138923893389438953896389738983899390039013902390339043905390639073908390939103911391239133914391539163917391839193920392139223923392439253926392739283929393039313932393339343935393639373938393939403941394239433944394539463947394839493950395139523953395439553956395739583959396039613962396339643965396639673968396939703971397239733974397539763977397839793980398139823983398439853986398739883989399039913992399339943995399639973998399940004001400240034004400540064007400840094010401140124013401440154016401740184019402040214022402340244025402640274028402940304031403240334034403540364037403840394040404140424043404440454046404740484049405040514052405340544055405640574058405940604061406240634064406540664067406840694070407140724073407440754076407740784079408040814082408340844085408640874088408940904091409240934094409540964097409840994100410141024103410441054106410741084109411041114112411341144115411641174118411941204121412241234124412541264127412841294130413141324133413441354136413741384139414041414142414341444145414641474148414941504151415241534154415541564157415841594160416141624163416441654166416741684169417041714172417341744175417641774178417941804181418241834184418541864187418841894190419141924193419441954196419741984199420042014202420342044205420642074208420942104211421242134214421542164217421842194220422142224223422442254226422742284229423042314232423342344235423642374238423942404241424242434244424542464247424842494250425142524253425442554256425742584259426042614262426342644265426642674268426942704271427242734274427542764277427842794280428142824283428442854286428742884289429042914292429342944295429642974298429943004301430243034304430543064307430843094310431143124313431443154316431743184319432043214322432343244325432643274328432943304331433243334334433543364337433843394340434143424343434443454346434743484349435043514352435343544355435643574358435943604361436243634364436543664367436843694370437143724373437443754376437743784379438043814382438343844385438643874388438943904391439243934394439543964397439843994400440144024403440444054406440744084409441044114412441344144415441644174418441944204421442244234424442544264427442844294430443144324433443444354436443744384439444044414442444344444445444644474448444944504451445244534454445544564457445844594460446144624463446444654466446744684469447044714472447344744475447644774478447944804481448244834484448544864487448844894490449144924493449444954496449744984499450045014502450345044505450645074508450945104511451245134514451545164517451845194520452145224523452445254526452745284529453045314532453345344535453645374538453945404541454245434544454545464547454845494550455145524553455445554556455745584559456045614562456345644565456645674568456945704571457245734574457545764577457845794580458145824583458445854586458745884589459045914592459345944595459645974598459946004601460246034604460546064607460846094610461146124613461446154616461746184619462046214622462346244625462646274628462946304631463246334634463546364637463846394640464146424643464446454646464746484649465046514652465346544655465646574658465946604661466246634664466546664667466846694670467146724673467446754676467746784679468046814682468346844685468646874688468946904691469246934694469546964697469846994700470147024703470447054706470747084709471047114712471347144715471647174718471947204721472247234724472547264727472847294730473147324733473447354736473747384739474047414742474347444745474647474748474947504751475247534754475547564757475847594760476147624763476447654766476747684769477047714772477347744775477647774778477947804781478247834784478547864787478847894790479147924793479447954796479747984799480048014802480348044805480648074808480948104811481248134814481548164817481848194820482148224823482448254826482748284829483048314832483348344835483648374838483948404841484248434844484548464847484848494850485148524853485448554856485748584859486048614862486348644865486648674868486948704871487248734874487548764877487848794880488148824883488448854886488748884889489048914892489348944895489648974898489949004901490249034904490549064907490849094910491149124913491449154916491749184919492049214922492349244925492649274928492949304931493249334934493549364937493849394940494149424943494449454946494749484949495049514952495349544955495649574958495949604961496249634964496549664967496849694970497149724973497449754976497749784979498049814982498349844985498649874988498949904991499249934994499549964997499849995000500150025003500450055006500750085009501050115012501350145015501650175018501950205021502250235024502550265027502850295030503150325033503450355036503750385039504050415042504350445045504650475048504950505051505250535054505550565057505850595060506150625063506450655066506750685069507050715072507350745075507650775078507950805081508250835084508550865087508850895090509150925093509450955096509750985099510051015102510351045105510651075108510951105111511251135114511551165117511851195120512151225123512451255126512751285129513051315132513351345135513651375138513951405141514251435144514551465147514851495150515151525153515451555156515751585159516051615162516351645165516651675168516951705171517251735174517551765177517851795180518151825183518451855186518751885189519051915192519351945195519651975198519952005201520252035204520552065207520852095210521152125213521452155216521752185219522052215222522352245225522652275228522952305231523252335234523552365237523852395240524152425243524452455246524752485249525052515252525352545255525652575258525952605261526252635264526552665267526852695270527152725273527452755276527752785279528052815282528352845285528652875288528952905291529252935294529552965297529852995300530153025303530453055306530753085309531053115312531353145315531653175318531953205321532253235324532553265327532853295330533153325333533453355336533753385339534053415342534353445345534653475348534953505351535253535354535553565357535853595360536153625363536453655366536753685369537053715372537353745375537653775378537953805381538253835384538553865387538853895390539153925393539453955396539753985399540054015402540354045405540654075408540954105411541254135414541554165417541854195420542154225423542454255426542754285429543054315432543354345435543654375438543954405441544254435444544554465447544854495450545154525453545454555456545754585459546054615462546354645465546654675468546954705471547254735474547554765477547854795480548154825483548454855486548754885489549054915492549354945495549654975498549955005501550255035504550555065507550855095510551155125513551455155516551755185519552055215522552355245525552655275528552955305531553255335534553555365537553855395540554155425543554455455546554755485549555055515552555355545555555655575558555955605561556255635564556555665567556855695570557155725573557455755576557755785579558055815582558355845585558655875588558955905591559255935594559555965597559855995600560156025603560456055606560756085609561056115612561356145615561656175618561956205621562256235624562556265627562856295630563156325633563456355636563756385639564056415642564356445645564656475648564956505651565256535654565556565657565856595660566156625663566456655666566756685669567056715672567356745675567656775678567956805681568256835684568556865687568856895690569156925693569456955696569756985699570057015702570357045705570657075708570957105711571257135714571557165717571857195720572157225723572457255726572757285729573057315732573357345735573657375738573957405741574257435744574557465747574857495750575157525753575457555756575757585759576057615762576357645765576657675768576957705771577257735774577557765777577857795780578157825783578457855786578757885789579057915792579357945795579657975798579958005801580258035804580558065807580858095810581158125813581458155816581758185819582058215822582358245825582658275828582958305831583258335834583558365837583858395840584158425843584458455846584758485849585058515852585358545855585658575858585958605861586258635864586558665867586858695870587158725873587458755876587758785879588058815882588358845885588658875888588958905891589258935894589558965897589858995900590159025903590459055906590759085909591059115912591359145915591659175918591959205921592259235924592559265927592859295930593159325933593459355936593759385939594059415942594359445945594659475948594959505951595259535954595559565957595859595960596159625963596459655966596759685969597059715972597359745975597659775978597959805981598259835984598559865987598859895990599159925993599459955996599759985999600060016002600360046005600660076008600960106011601260136014601560166017601860196020602160226023602460256026602760286029603060316032603360346035603660376038603960406041604260436044604560466047604860496050605160526053605460556056605760586059606060616062606360646065606660676068606960706071607260736074607560766077607860796080608160826083608460856086608760886089609060916092609360946095609660976098609961006101610261036104610561066107610861096110611161126113611461156116611761186119612061216122612361246125612661276128612961306131613261336134613561366137613861396140614161426143614461456146614761486149615061516152615361546155615661576158615961606161616261636164616561666167616861696170617161726173617461756176617761786179618061816182618361846185618661876188618961906191619261936194619561966197619861996200620162026203620462056206620762086209621062116212621362146215621662176218621962206221622262236224622562266227622862296230623162326233623462356236623762386239624062416242624362446245624662476248624962506251625262536254625562566257625862596260626162626263626462656266626762686269627062716272627362746275627662776278627962806281628262836284628562866287628862896290629162926293629462956296629762986299630063016302630363046305630663076308630963106311631263136314631563166317631863196320632163226323632463256326632763286329633063316332633363346335633663376338633963406341634263436344634563466347634863496350635163526353635463556356635763586359636063616362636363646365636663676368636963706371637263736374637563766377637863796380638163826383638463856386638763886389639063916392639363946395639663976398639964006401640264036404640564066407640864096410641164126413641464156416641764186419642064216422642364246425642664276428642964306431643264336434643564366437643864396440644164426443644464456446644764486449645064516452645364546455645664576458645964606461646264636464646564666467646864696470647164726473647464756476647764786479648064816482648364846485648664876488648964906491649264936494649564966497649864996500650165026503650465056506650765086509651065116512651365146515651665176518651965206521652265236524652565266527652865296530653165326533653465356536653765386539654065416542654365446545654665476548654965506551655265536554655565566557655865596560656165626563656465656566656765686569657065716572657365746575657665776578657965806581658265836584658565866587658865896590659165926593659465956596659765986599660066016602660366046605660666076608660966106611661266136614661566166617661866196620662166226623662466256626662766286629663066316632663366346635663666376638663966406641664266436644664566466647664866496650665166526653665466556656665766586659666066616662666366646665666666676668666966706671667266736674667566766677667866796680668166826683668466856686668766886689669066916692669366946695669666976698669967006701670267036704670567066707670867096710671167126713671467156716671767186719672067216722672367246725672667276728672967306731673267336734673567366737673867396740674167426743674467456746674767486749675067516752675367546755675667576758675967606761676267636764676567666767676867696770677167726773677467756776677767786779678067816782678367846785678667876788678967906791679267936794679567966797679867996800680168026803680468056806680768086809681068116812681368146815681668176818681968206821682268236824682568266827682868296830683168326833683468356836683768386839684068416842684368446845684668476848684968506851685268536854685568566857685868596860686168626863686468656866686768686869687068716872687368746875687668776878687968806881688268836884688568866887688868896890689168926893689468956896689768986899690069016902690369046905690669076908690969106911691269136914691569166917691869196920692169226923692469256926692769286929693069316932693369346935693669376938693969406941694269436944694569466947694869496950695169526953695469556956695769586959696069616962696369646965696669676968696969706971697269736974697569766977697869796980698169826983698469856986698769886989699069916992699369946995699669976998699970007001700270037004700570067007700870097010701170127013701470157016701770187019702070217022702370247025702670277028702970307031703270337034703570367037703870397040704170427043704470457046704770487049705070517052705370547055705670577058705970607061706270637064706570667067706870697070707170727073707470757076707770787079708070817082708370847085708670877088708970907091709270937094709570967097709870997100710171027103710471057106710771087109711071117112711371147115711671177118711971207121712271237124712571267127712871297130713171327133713471357136713771387139714071417142714371447145714671477148714971507151715271537154715571567157715871597160716171627163716471657166716771687169717071717172717371747175717671777178717971807181718271837184718571867187718871897190719171927193719471957196719771987199720072017202720372047205720672077208720972107211721272137214721572167217721872197220722172227223722472257226722772287229723072317232723372347235723672377238723972407241724272437244724572467247724872497250725172527253725472557256725772587259726072617262726372647265726672677268726972707271727272737274727572767277727872797280728172827283728472857286728772887289729072917292729372947295729672977298729973007301730273037304730573067307730873097310731173127313731473157316731773187319732073217322732373247325732673277328732973307331733273337334733573367337733873397340734173427343734473457346734773487349735073517352735373547355735673577358735973607361736273637364736573667367736873697370737173727373737473757376737773787379738073817382738373847385738673877388738973907391739273937394739573967397739873997400740174027403740474057406740774087409741074117412741374147415741674177418741974207421742274237424742574267427742874297430743174327433743474357436743774387439744074417442744374447445744674477448744974507451745274537454745574567457745874597460746174627463746474657466746774687469747074717472747374747475747674777478747974807481748274837484748574867487748874897490749174927493749474957496749774987499750075017502750375047505750675077508750975107511751275137514751575167517751875197520752175227523752475257526752775287529753075317532753375347535753675377538753975407541754275437544754575467547754875497550755175527553755475557556755775587559756075617562756375647565756675677568756975707571757275737574757575767577757875797580758175827583758475857586758775887589759075917592759375947595759675977598759976007601760276037604760576067607760876097610761176127613761476157616761776187619762076217622762376247625762676277628762976307631763276337634763576367637763876397640764176427643764476457646764776487649765076517652765376547655765676577658765976607661766276637664766576667667766876697670767176727673767476757676767776787679768076817682768376847685768676877688768976907691769276937694769576967697769876997700770177027703770477057706770777087709771077117712771377147715771677177718771977207721772277237724772577267727772877297730773177327733773477357736773777387739774077417742774377447745774677477748774977507751775277537754775577567757775877597760776177627763776477657766776777687769777077717772777377747775777677777778777977807781778277837784778577867787778877897790779177927793779477957796779777987799780078017802780378047805780678077808780978107811781278137814781578167817781878197820782178227823782478257826782778287829783078317832783378347835783678377838783978407841784278437844784578467847784878497850785178527853785478557856785778587859786078617862786378647865786678677868786978707871787278737874787578767877787878797880788178827883788478857886788778887889789078917892789378947895789678977898789979007901790279037904790579067907790879097910791179127913791479157916791779187919792079217922792379247925792679277928792979307931793279337934793579367937793879397940794179427943794479457946794779487949795079517952795379547955795679577958795979607961796279637964796579667967796879697970797179727973797479757976797779787979798079817982798379847985798679877988798979907991799279937994799579967997799879998000800180028003800480058006800780088009801080118012801380148015801680178018801980208021802280238024802580268027802880298030803180328033803480358036803780388039804080418042804380448045804680478048804980508051805280538054805580568057805880598060806180628063806480658066806780688069807080718072807380748075807680778078807980808081808280838084808580868087808880898090809180928093809480958096809780988099810081018102810381048105810681078108810981108111811281138114811581168117811881198120812181228123812481258126812781288129813081318132813381348135813681378138813981408141814281438144814581468147814881498150815181528153815481558156815781588159816081618162816381648165816681678168816981708171817281738174817581768177817881798180818181828183818481858186818781888189819081918192819381948195819681978198819982008201820282038204820582068207820882098210821182128213821482158216821782188219822082218222822382248225822682278228822982308231823282338234823582368237823882398240824182428243824482458246824782488249825082518252825382548255825682578258825982608261826282638264826582668267826882698270827182728273827482758276827782788279828082818282828382848285828682878288828982908291829282938294829582968297829882998300830183028303830483058306830783088309831083118312831383148315831683178318831983208321832283238324832583268327832883298330833183328333833483358336833783388339834083418342834383448345834683478348834983508351835283538354835583568357835883598360836183628363836483658366836783688369837083718372837383748375837683778378837983808381838283838384838583868387838883898390839183928393839483958396839783988399840084018402840384048405840684078408840984108411841284138414841584168417841884198420842184228423842484258426842784288429843084318432843384348435843684378438843984408441844284438444844584468447844884498450845184528453845484558456845784588459846084618462846384648465846684678468846984708471847284738474847584768477847884798480848184828483848484858486848784888489849084918492849384948495849684978498849985008501850285038504850585068507850885098510851185128513851485158516851785188519852085218522852385248525852685278528852985308531853285338534853585368537853885398540854185428543854485458546854785488549855085518552855385548555855685578558855985608561856285638564856585668567856885698570857185728573857485758576857785788579858085818582858385848585858685878588858985908591859285938594859585968597859885998600860186028603860486058606860786088609861086118612861386148615861686178618861986208621862286238624862586268627862886298630863186328633863486358636863786388639864086418642864386448645864686478648864986508651865286538654865586568657865886598660866186628663866486658666866786688669867086718672867386748675867686778678867986808681868286838684868586868687868886898690869186928693869486958696869786988699870087018702870387048705870687078708870987108711871287138714871587168717871887198720872187228723872487258726872787288729873087318732873387348735873687378738873987408741874287438744874587468747874887498750875187528753875487558756875787588759876087618762876387648765876687678768876987708771877287738774877587768777877887798780878187828783878487858786878787888789879087918792879387948795879687978798879988008801880288038804880588068807880888098810881188128813881488158816881788188819882088218822882388248825882688278828882988308831883288338834883588368837883888398840884188428843884488458846884788488849885088518852885388548855885688578858885988608861886288638864886588668867886888698870887188728873887488758876887788788879888088818882888388848885888688878888888988908891889288938894889588968897889888998900890189028903890489058906890789088909891089118912891389148915891689178918891989208921892289238924892589268927892889298930893189328933893489358936893789388939894089418942894389448945894689478948894989508951895289538954895589568957895889598960896189628963896489658966896789688969897089718972897389748975897689778978897989808981898289838984898589868987898889898990899189928993899489958996899789988999900090019002900390049005900690079008900990109011901290139014901590169017901890199020902190229023902490259026902790289029903090319032903390349035903690379038903990409041904290439044904590469047904890499050905190529053905490559056905790589059906090619062906390649065906690679068906990709071907290739074907590769077907890799080908190829083908490859086908790889089909090919092909390949095909690979098909991009101910291039104910591069107910891099110911191129113911491159116911791189119912091219122912391249125912691279128912991309131913291339134913591369137913891399140914191429143914491459146914791489149915091519152915391549155915691579158915991609161916291639164916591669167916891699170917191729173917491759176917791789179918091819182918391849185918691879188918991909191919291939194919591969197919891999200920192029203920492059206920792089209921092119212921392149215921692179218921992209221922292239224922592269227922892299230923192329233923492359236923792389239924092419242924392449245924692479248924992509251925292539254925592569257925892599260926192629263926492659266926792689269927092719272927392749275927692779278927992809281928292839284928592869287928892899290929192929293929492959296929792989299930093019302930393049305930693079308930993109311931293139314931593169317931893199320932193229323932493259326932793289329933093319332933393349335933693379338933993409341934293439344934593469347934893499350935193529353935493559356935793589359936093619362936393649365936693679368936993709371937293739374937593769377937893799380938193829383938493859386938793889389939093919392939393949395939693979398939994009401940294039404940594069407940894099410941194129413941494159416941794189419942094219422942394249425942694279428942994309431943294339434943594369437943894399440944194429443944494459446944794489449945094519452945394549455945694579458945994609461946294639464946594669467946894699470947194729473947494759476947794789479948094819482948394849485948694879488948994909491949294939494949594969497949894999500950195029503950495059506950795089509951095119512951395149515951695179518951995209521952295239524952595269527952895299530953195329533953495359536953795389539954095419542954395449545954695479548954995509551955295539554955595569557955895599560956195629563956495659566956795689569957095719572957395749575957695779578957995809581958295839584958595869587958895899590959195929593959495959596959795989599960096019602960396049605960696079608960996109611961296139614961596169617961896199620962196229623962496259626962796289629963096319632963396349635963696379638963996409641964296439644964596469647964896499650965196529653965496559656965796589659966096619662966396649665966696679668966996709671967296739674967596769677967896799680968196829683968496859686968796889689969096919692969396949695969696979698969997009701970297039704970597069707970897099710971197129713971497159716971797189719972097219722972397249725972697279728972997309731973297339734973597369737973897399740974197429743974497459746974797489749975097519752975397549755975697579758975997609761976297639764976597669767976897699770977197729773977497759776977797789779978097819782978397849785978697879788978997909791979297939794979597969797979897999800980198029803980498059806980798089809981098119812981398149815981698179818981998209821982298239824982598269827982898299830983198329833983498359836983798389839984098419842984398449845984698479848984998509851985298539854985598569857985898599860986198629863986498659866986798689869987098719872987398749875987698779878987998809881988298839884988598869887988898899890989198929893989498959896989798989899990099019902990399049905990699079908990999109911991299139914991599169917991899199920992199229923992499259926992799289929993099319932993399349935993699379938993999409941994299439944994599469947994899499950995199529953995499559956995799589959996099619962996399649965996699679968996999709971997299739974997599769977997899799980998199829983998499859986998799889989999099919992999399949995999699979998999910000100011000210003100041000510006100071000810009100101001110012100131001410015100161001710018100191002010021100221002310024100251002610027100281002910030100311003210033100341003510036100371003810039100401004110042100431004410045100461004710048100491005010051100521005310054100551005610057100581005910060100611006210063100641006510066100671006810069100701007110072100731007410075100761007710078100791008010081100821008310084100851008610087100881008910090100911009210093100941009510096100971009810099101001010110102101031010410105101061010710108101091011010111101121011310114101151011610117101181011910120101211012210123101241012510126101271012810129101301013110132101331013410135101361013710138101391014010141101421014310144101451014610147101481014910150101511015210153101541015510156101571015810159101601016110162101631016410165101661016710168101691017010171101721017310174101751017610177101781017910180101811018210183101841018510186101871018810189101901019110192101931019410195101961019710198101991020010201102021020310204102051020610207102081020910210102111021210213102141021510216102171021810219102201022110222102231022410225102261022710228102291023010231102321023310234102351023610237102381023910240102411024210243102441024510246102471024810249102501025110252102531025410255102561025710258102591026010261102621026310264102651026610267102681026910270102711027210273102741027510276102771027810279102801028110282102831028410285102861028710288102891029010291102921029310294102951029610297102981029910300103011030210303103041030510306103071030810309103101031110312103131031410315103161031710318103191032010321103221032310324103251032610327103281032910330103311033210333103341033510336103371033810339103401034110342103431034410345103461034710348103491035010351103521035310354103551035610357103581035910360103611036210363103641036510366103671036810369103701037110372103731037410375103761037710378103791038010381103821038310384103851038610387103881038910390103911039210393103941039510396103971039810399104001040110402104031040410405104061040710408104091041010411104121041310414104151041610417104181041910420104211042210423104241042510426104271042810429104301043110432104331043410435104361043710438104391044010441104421044310444104451044610447104481044910450104511045210453104541045510456104571045810459104601046110462104631046410465104661046710468104691047010471104721047310474104751047610477104781047910480104811048210483104841048510486104871048810489104901049110492104931049410495104961049710498104991050010501105021050310504105051050610507105081050910510105111051210513105141051510516105171051810519105201052110522105231052410525105261052710528105291053010531105321053310534105351053610537105381053910540105411054210543105441054510546105471054810549105501055110552105531055410555105561055710558105591056010561105621056310564105651056610567105681056910570105711057210573105741057510576105771057810579105801058110582105831058410585105861058710588105891059010591105921059310594105951059610597105981059910600106011060210603106041060510606106071060810609106101061110612106131061410615106161061710618106191062010621106221062310624106251062610627106281062910630106311063210633106341063510636106371063810639106401064110642106431064410645106461064710648106491065010651106521065310654106551065610657106581065910660106611066210663106641066510666106671066810669106701067110672106731067410675106761067710678106791068010681106821068310684106851068610687106881068910690106911069210693106941069510696106971069810699107001070110702107031070410705107061070710708107091071010711107121071310714107151071610717107181071910720107211072210723107241072510726107271072810729107301073110732107331073410735107361073710738107391074010741107421074310744107451074610747107481074910750107511075210753107541075510756107571075810759107601076110762107631076410765107661076710768107691077010771107721077310774107751077610777107781077910780107811078210783107841078510786107871078810789107901079110792107931079410795107961079710798107991080010801108021080310804108051080610807108081080910810108111081210813108141081510816108171081810819108201082110822108231082410825108261082710828108291083010831108321083310834108351083610837108381083910840108411084210843108441084510846108471084810849108501085110852108531085410855108561085710858108591086010861108621086310864108651086610867108681086910870108711087210873108741087510876108771087810879108801088110882108831088410885108861088710888108891089010891108921089310894108951089610897108981089910900109011090210903109041090510906109071090810909109101091110912109131091410915 |
- Thu Aug 8 10:53:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/other/t2w001.nii.gz -T2pial -subjid sub002 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub002
- 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 96466116 2735576 0 177872 94401912
- -/+ buffers/cache: 1886332 97315360
- 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/sub002
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999032, 0.0218052, 0.0381938)
- j_ras = (0.0265301, 0.991428, 0.127932)
- k_ras = (0.0350768, -0.128822, 0.991047)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999032, 0.0218052, 0.0381938)
- j_ras = (0.0265301, 0.991428, 0.127932)
- k_ras = (0.0350768, -0.128822, 0.991047)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:34 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999032, 0.0218052, 0.0381938)
- j_ras = (0.0265301, 0.991428, 0.127932)
- k_ras = (0.0350768, -0.128822, 0.991047)
- Original Data has (0.69986, 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/sub002/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 10:58:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6149, pval=0.2817 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach_avi.log
- TalAviQA: 0.96536
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:58:20 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/sub002/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 10:58:20 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.13482
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13482/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13482/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, 4.19095e-09, 0)
- j_ras = (0, 1.49012e-08, -1)
- k_ras = (0, 1, 0)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.13482/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:24 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.13482/nu0.mnc ./tmp.mri_nu_correct.mni.13482/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13482/0/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:58:24] 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.13482/0/ ./tmp.mri_nu_correct.mni.13482/nu0.mnc ./tmp.mri_nu_correct.mni.13482/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
- Number of iterations: 24
- CV of field change: 0.000983369
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:59:04] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13482/nu0.mnc ./tmp.mri_nu_correct.mni.13482/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:59:10 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.13482/nu1.mnc ./tmp.mri_nu_correct.mni.13482/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.13482/1/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:59:11] 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.13482/1/ ./tmp.mri_nu_correct.mni.13482/nu1.mnc ./tmp.mri_nu_correct.mni.13482/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
- Number of iterations: 19
- CV of field change: 0.000998983
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:59:43] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13482/nu1.mnc ./tmp.mri_nu_correct.mni.13482/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13482/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/sub002/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13482/ones.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.13482/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.13482/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.13482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/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.13482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/input.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.13482/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.13482/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13482/ones.mgz --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/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.13482/ones.mgz --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/output.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.13482/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.13482/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.13482/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.13482/nu2.mnc ./tmp.mri_nu_correct.mni.13482/nu2.mnc mul .95897357684828611735
- Saving result to './tmp.mri_nu_correct.mni.13482/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.13482/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.13482/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.13482/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.19095e-09, 0)
- j_ras = (0, 1.49012e-08, -1)
- k_ras = (0, 1, 0)
- 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, 186) to ( 3, 110)
-
-
- Thu Aug 8 11:00:37 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:00:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.074 0.029 -0.002 1.673;
- -0.085 0.995 0.325 -24.310;
- 0.058 -0.436 1.080 3.275;
- 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 = 17
- Starting OpenSpline(): npoints = 17
- 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 55 (55), valley at 44 (44)
- csf peak at 27, setting threshold to 45
- 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 58 (58), valley at 46 (46)
- csf peak at 10, setting threshold to 42
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 50 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:03:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = (48, 14, 9) --> (203, 255, 206)
- using (100, 94, 108) as brain centroid...
- mean wm in atlas = 126, using box (81,64,84) --> (119, 123,132) to find MRI wm
- before smoothing, mri peak at 109
- 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 = -4.516131 @ (-9.091, 27.273, -9.091)
- max log p = -4.328604 @ (4.545, -4.545, -4.545)
- max log p = -4.280679 @ (6.818, 2.273, 2.273)
- max log p = -4.239203 @ (-3.409, -1.136, 3.409)
- max log p = -4.239203 @ (0.000, 0.000, 0.000)
- max log p = -4.239203 @ (0.000, 0.000, 0.000)
- Found translation: (-1.1, 23.9, -8.0): log p = -4.239
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2)
- 1.000 0.000 0.000 -1.136;
- 0.000 1.111 0.298 -20.841;
- 0.000 -0.259 0.966 21.099;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.000 0.000 0.000 -1.136;
- 0.000 1.111 0.298 -20.841;
- 0.000 -0.259 0.966 21.099;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.037 0.010 -0.031 -3.322;
- 0.000 1.081 0.323 -19.077;
- 0.033 -0.289 0.937 26.785;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.037 0.010 -0.031 -3.322;
- 0.000 1.081 0.323 -19.077;
- 0.033 -0.289 0.937 26.785;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.040 0.014 -0.013 -5.550;
- -0.008 1.074 0.338 -19.449;
- 0.016 -0.308 0.933 31.166;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.037 0.007 -0.024 -3.947;
- 0.001 1.072 0.337 -20.348;
- 0.025 -0.309 0.936 29.822;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.037 0.007 -0.024 -3.947;
- 0.001 1.072 0.337 -20.348;
- 0.025 -0.309 0.937 29.733;
- 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
- 1.03718 0.00722 -0.02361 -3.94694;
- 0.00063 1.07237 0.33720 -20.34751;
- 0.02498 -0.30908 0.93747 29.73334;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.03718 0.00722 -0.02361 -3.94694;
- 0.00063 1.07237 0.33720 -20.34751;
- 0.02498 -0.30908 0.93747 29.73334;
- 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:
- 1.037 0.007 -0.024 -3.947;
- 0.001 1.072 0.337 -20.348;
- 0.025 -0.309 0.937 29.733;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.8)
- transform before final EM align:
- 1.037 0.007 -0.024 -3.947;
- 0.001 1.072 0.337 -20.348;
- 0.025 -0.309 0.937 29.733;
- 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
- 1.03718 0.00722 -0.02361 -3.94694;
- 0.00063 1.07237 0.33720 -20.34751;
- 0.02498 -0.30908 0.93747 29.73334;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.03718 0.00722 -0.02361 -3.94694;
- 0.00063 1.07237 0.33720 -20.34751;
- 0.02498 -0.30908 0.93747 29.73334;
- 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: 011: -log(p) = 4.3 tol 0.000000
- final transform:
- 1.037 0.007 -0.024 -3.947;
- 0.001 1.072 0.337 -20.348;
- 0.025 -0.309 0.937 29.733;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 34 minutes and 35 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=127 y=82 z=115 r=95
- first estimation of the main basin volume: 3669857 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 18 found in the rest of the brain
- global maximum in x=106, y=83, z=72, Imax=255
- CSF=12, WM_intensity=110, WM_VARIANCE=5
- WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
- preflooding height equal to 10 percent
- done.
- Analyze...
- main basin size=22454927539 voxels, voxel volume =1.000
- = 22454927539 mmm3 = 22454927.360 cm3
- done.
- PostAnalyze...Basin Prior
- 101 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=96, z=109, r=10759 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 45624
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=11 , nb = -1030081359
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1085671112
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1077613020
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1080297068
- OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=20 , nb = 1078030124
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 5, 6, 23, 57
- after analyzing : 5, 18, 25, 27
- RIGHT_CER
- before analyzing : 11, 14, 28, 61
- after analyzing : 11, 23, 28, 32
- LEFT_CER
- before analyzing : 5, 7, 31, 60
- after analyzing : 5, 23, 31, 32
- RIGHT_BRAIN
- before analyzing : 4, 4, 20, 56
- after analyzing : 4, 18, 25, 27
- LEFT_BRAIN
- before analyzing : 4, 4, 22, 57
- after analyzing : 4, 18, 25, 27
- OTHER
- before analyzing : 20, 56, 83, 95
- after analyzing : 20, 74, 83, 79
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...73 iterations
- *********************VALIDATION*********************
- curvature mean = -0.012, std = 0.011
- curvature mean = 74.768, std = 9.612
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 2.57, sigma = 4.37
- after rotation: sse = 2.57, sigma = 4.37
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 2.70, its var is 4.15
- before Erosion-Dilatation 0.61% 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...37 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 2059915 voxels, voxel volume = 1.000 mm3
- = 2059915 mmm3 = 2059.915 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:38:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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=19.0
- skull bounding box = (58, 29, 30) --> (192, 180, 201)
- using (103, 79, 116) as brain centroid...
- mean wm in atlas = 107, using box (87,60,95) --> (119, 97,137) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 109, scaling input intensities by 0.982
- scaling channel 0 by 0.981651
- initial log_p = -4.4
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.067876 @ (-9.091, 27.273, -9.091)
- max log p = -3.863126 @ (4.545, -4.545, -4.545)
- max log p = -3.785619 @ (2.273, -2.273, 6.818)
- max log p = -3.774508 @ (-1.136, 1.136, -3.409)
- max log p = -3.746221 @ (1.705, 0.568, 1.705)
- max log p = -3.746221 @ (0.000, 0.000, 0.000)
- Found translation: (-1.7, 22.2, -8.5): log p = -3.746
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.3, old_max_log_p =-3.7 (thresh=-3.7)
- 1.000 0.000 0.000 -1.705;
- 0.000 1.028 0.275 -11.845;
- 0.000 -0.236 0.883 27.712;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.000 0.000 0.000 -1.705;
- 0.000 1.028 0.275 -11.845;
- 0.000 -0.236 0.883 27.712;
- 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=-3.2, old_max_log_p =-3.3 (thresh=-3.3)
- 1.037 0.007 -0.030 -3.554;
- 0.002 1.038 0.311 -15.194;
- 0.034 -0.279 0.906 28.550;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.037 0.007 -0.030 -3.554;
- 0.002 1.038 0.311 -15.194;
- 0.034 -0.279 0.906 28.550;
- 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 =-3.2 (thresh=-3.2)
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 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=-3.1)
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 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
- 1.03451 0.00692 -0.03020 -3.24805;
- 0.00226 1.03926 0.31115 -15.35058;
- 0.03379 -0.27772 0.90255 29.75585;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.03451 0.00692 -0.03020 -3.24805;
- 0.00226 1.03926 0.31115 -15.35058;
- 0.03379 -0.27772 0.90255 29.75585;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.2 (old=-4.4)
- transform before final EM align:
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 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
- 1.03451 0.00692 -0.03020 -3.24805;
- 0.00226 1.03926 0.31115 -15.35058;
- 0.03379 -0.27772 0.90255 29.75585;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.03451 0.00692 -0.03020 -3.24805;
- 0.00226 1.03926 0.31115 -15.35058;
- 0.03379 -0.27772 0.90255 29.75585;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 009: -log(p) = 3.8
- after pass:transform: ( 1.03, 0.01, -0.03, -3.25)
- ( 0.00, 1.04, 0.31, -15.35)
- ( 0.03, -0.28, 0.90, 29.76)
- dfp_em_step_func: 010: -log(p) = 3.8
- after pass:transform: ( 1.03, 0.01, -0.03, -3.25)
- ( 0.00, 1.04, 0.31, -15.35)
- ( 0.03, -0.28, 0.90, 29.76)
- dfp_em_step_func: 011: -log(p) = 3.8
- after pass:transform: ( 1.03, 0.01, -0.03, -3.25)
- ( 0.00, 1.04, 0.31, -15.35)
- ( 0.03, -0.28, 0.90, 29.76)
- dfp_em_step_func: 012: -log(p) = 3.8
- after pass:transform: ( 1.03, 0.01, -0.03, -3.25)
- ( 0.00, 1.04, 0.31, -15.35)
- ( 0.03, -0.28, 0.90, 29.76)
- 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 TOLERANCESpass 2 through quasi-newton minimization...
- 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: 014: -log(p) = 3.8 tol 0.000000
- final transform:
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 24 minutes and 39 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:03:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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=19.0
- skull bounding box = (58, 29, 30) --> (192, 180, 201)
- using (103, 79, 116) as brain centroid...
- mean wm in atlas = 107, using box (87,60,95) --> (119, 97,137) to find MRI wm
- before smoothing, mri peak at 109
- 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
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 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 (123, 35, 29) --> (191, 147, 201)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 143.0
- 0 of 18 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (65, 34, 30) --> (129, 138, 203)
- Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 143.0
- 0 of 18 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (128, 119, 61) --> (175, 162, 116)
- Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 143.0
- 0 of 9 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (82, 119, 59) --> (127, 160, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 143.0
- 3 of 9 (33.3%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (112, 107, 96) --> (143, 172, 128)
- Brain_Stem: limiting intensities to 91.0 --> 143.0
- 5 of 10 (50.0%) samples deleted
- using 64 total control points for intensity normalization...
- bias field = 0.990 +- 0.066
- 0 of 56 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (123, 35, 29) --> (191, 147, 201)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 136.0
- 0 of 112 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (65, 34, 30) --> (129, 138, 203)
- Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 136.0
- 0 of 77 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (128, 119, 61) --> (175, 162, 116)
- Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 136.0
- 0 of 28 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (82, 119, 59) --> (127, 160, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 136.0
- 0 of 42 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (112, 107, 96) --> (143, 172, 128)
- Brain_Stem: limiting intensities to 87.0 --> 136.0
- 21 of 66 (31.8%) samples deleted
- using 325 total control points for intensity normalization...
- bias field = 0.983 +- 0.048
- 0 of 304 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (123, 35, 29) --> (191, 147, 201)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 134.0
- 1 of 201 (0.5%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (65, 34, 30) --> (129, 138, 203)
- Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 134.0
- 0 of 213 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (128, 119, 61) --> (175, 162, 116)
- Left_Cerebellum_White_Matter: limiting intensities to 76.0 --> 134.0
- 0 of 43 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (82, 119, 59) --> (127, 160, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 76.0 --> 134.0
- 0 of 43 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (112, 107, 96) --> (143, 172, 128)
- Brain_Stem: limiting intensities to 74.0 --> 134.0
- 0 of 80 (0.0%) samples deleted
- using 580 total control points for intensity normalization...
- bias field = 1.009 +- 0.045
- 1 of 579 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 4 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:05:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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) = 1.06 (predicted orig area = 7.5)
- 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=0.869, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.799 (8.041%), neg=0, invalid=96777
- 0002: dt=110.976000, rms=0.791 (1.042%), neg=0, invalid=96777
- 0003: dt=129.472000, rms=0.780 (1.290%), neg=0, invalid=96777
- 0004: dt=129.472000, rms=0.778 (0.344%), neg=0, invalid=96777
- 0005: dt=221.952000, rms=0.770 (1.002%), neg=0, invalid=96777
- 0006: dt=32.368000, rms=0.768 (0.224%), neg=0, invalid=96777
- 0007: dt=32.368000, rms=0.767 (0.104%), neg=0, invalid=96777
- 0008: dt=32.368000, rms=0.767 (0.098%), neg=0, invalid=96777
- 0009: dt=32.368000, rms=0.766 (0.128%), neg=0, invalid=96777
- 0010: dt=32.368000, rms=0.764 (0.245%), neg=0, invalid=96777
- 0011: dt=32.368000, rms=0.761 (0.376%), neg=0, invalid=96777
- 0012: dt=32.368000, rms=0.758 (0.412%), neg=0, invalid=96777
- 0013: dt=32.368000, rms=0.755 (0.361%), neg=0, invalid=96777
- 0014: dt=32.368000, rms=0.753 (0.295%), neg=0, invalid=96777
- 0015: dt=32.368000, rms=0.751 (0.271%), neg=0, invalid=96777
- 0016: dt=32.368000, rms=0.749 (0.260%), neg=0, invalid=96777
- 0017: dt=32.368000, rms=0.747 (0.203%), neg=0, invalid=96777
- 0018: dt=32.368000, rms=0.746 (0.174%), neg=0, invalid=96777
- 0019: dt=32.368000, rms=0.744 (0.195%), neg=0, invalid=96777
- 0020: dt=32.368000, rms=0.743 (0.225%), neg=0, invalid=96777
- 0021: dt=32.368000, rms=0.741 (0.229%), neg=0, invalid=96777
- 0022: dt=32.368000, rms=0.740 (0.188%), neg=0, invalid=96777
- 0023: dt=32.368000, rms=0.738 (0.180%), neg=0, invalid=96777
- 0024: dt=32.368000, rms=0.737 (0.178%), neg=0, invalid=96777
- 0025: dt=32.368000, rms=0.736 (0.162%), neg=0, invalid=96777
- 0026: dt=32.368000, rms=0.735 (0.144%), neg=0, invalid=96777
- 0027: dt=32.368000, rms=0.734 (0.143%), neg=0, invalid=96777
- 0028: dt=32.368000, rms=0.733 (0.159%), neg=0, invalid=96777
- 0029: dt=32.368000, rms=0.731 (0.170%), neg=0, invalid=96777
- 0030: dt=32.368000, rms=0.730 (0.169%), neg=0, invalid=96777
- 0031: dt=32.368000, rms=0.729 (0.145%), neg=0, invalid=96777
- 0032: dt=32.368000, rms=0.728 (0.135%), neg=0, invalid=96777
- 0033: dt=32.368000, rms=0.727 (0.125%), neg=0, invalid=96777
- 0034: dt=32.368000, rms=0.726 (0.116%), neg=0, invalid=96777
- 0035: dt=32.368000, rms=0.726 (0.105%), neg=0, invalid=96777
- 0036: dt=1479.680000, rms=0.722 (0.481%), neg=0, invalid=96777
- 0037: dt=32.368000, rms=0.721 (0.141%), neg=0, invalid=96777
- 0038: dt=32.368000, rms=0.721 (0.036%), neg=0, invalid=96777
- 0039: dt=32.368000, rms=0.721 (-0.015%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.721, neg=0, invalid=96777
- 0040: dt=73.984000, rms=0.720 (0.075%), neg=0, invalid=96777
- 0041: dt=295.936000, rms=0.719 (0.186%), neg=0, invalid=96777
- 0042: dt=443.904000, rms=0.718 (0.153%), neg=0, invalid=96777
- 0043: dt=443.904000, rms=0.718 (-0.118%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.722, neg=0, invalid=96777
- 0044: dt=145.152000, rms=0.704 (2.480%), neg=0, invalid=96777
- 0045: dt=124.416000, rms=0.694 (1.496%), neg=0, invalid=96777
- 0046: dt=25.920000, rms=0.688 (0.745%), neg=0, invalid=96777
- 0047: dt=145.152000, rms=0.681 (1.090%), neg=0, invalid=96777
- 0048: dt=36.288000, rms=0.678 (0.408%), neg=0, invalid=96777
- 0049: dt=145.152000, rms=0.672 (0.838%), neg=0, invalid=96777
- 0050: dt=15.552000, rms=0.671 (0.263%), neg=0, invalid=96777
- 0051: dt=36.288000, rms=0.670 (0.136%), neg=0, invalid=96777
- 0052: dt=36.288000, rms=0.668 (0.251%), neg=0, invalid=96777
- 0053: dt=36.288000, rms=0.666 (0.305%), neg=0, invalid=96777
- 0054: dt=36.288000, rms=0.664 (0.363%), neg=0, invalid=96777
- 0055: dt=36.288000, rms=0.660 (0.476%), neg=0, invalid=96777
- 0056: dt=36.288000, rms=0.657 (0.588%), neg=0, invalid=96777
- 0057: dt=36.288000, rms=0.653 (0.557%), neg=0, invalid=96777
- 0058: dt=36.288000, rms=0.650 (0.483%), neg=0, invalid=96777
- 0059: dt=36.288000, rms=0.647 (0.448%), neg=0, invalid=96777
- 0060: dt=36.288000, rms=0.644 (0.463%), neg=0, invalid=96777
- 0061: dt=36.288000, rms=0.641 (0.428%), neg=0, invalid=96777
- 0062: dt=36.288000, rms=0.639 (0.360%), neg=0, invalid=96777
- 0063: dt=36.288000, rms=0.637 (0.300%), neg=0, invalid=96777
- 0064: dt=36.288000, rms=0.635 (0.317%), neg=0, invalid=96777
- 0065: dt=36.288000, rms=0.633 (0.291%), neg=0, invalid=96777
- 0066: dt=36.288000, rms=0.631 (0.240%), neg=0, invalid=96777
- 0067: dt=36.288000, rms=0.630 (0.205%), neg=0, invalid=96777
- 0068: dt=36.288000, rms=0.629 (0.202%), neg=0, invalid=96777
- 0069: dt=36.288000, rms=0.628 (0.196%), neg=0, invalid=96777
- 0070: dt=36.288000, rms=0.627 (0.141%), neg=0, invalid=96777
- 0071: dt=36.288000, rms=0.626 (0.097%), neg=0, invalid=96777
- 0072: dt=36.288000, rms=0.625 (0.114%), neg=0, invalid=96777
- 0073: dt=36.288000, rms=0.625 (0.149%), neg=0, invalid=96777
- 0074: dt=36.288000, rms=0.624 (0.137%), neg=0, invalid=96777
- 0075: dt=36.288000, rms=0.623 (0.113%), neg=0, invalid=96777
- 0076: dt=36.288000, rms=0.622 (0.111%), neg=0, invalid=96777
- 0077: dt=36.288000, rms=0.622 (0.007%), neg=0, invalid=96777
- 0078: dt=36.288000, rms=0.622 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.622, neg=0, invalid=96777
- 0079: dt=36.288000, rms=0.622 (0.052%), neg=0, invalid=96777
- 0080: dt=25.920000, rms=0.622 (0.014%), neg=0, invalid=96777
- 0081: dt=25.920000, rms=0.622 (-0.011%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.649, neg=0, invalid=96777
- 0082: dt=0.000000, rms=0.649 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.649, neg=0, invalid=96777
- 0083: dt=0.000000, rms=0.649 (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=0.730, neg=0, invalid=96777
- 0084: dt=4.939759, rms=0.707 (3.214%), neg=0, invalid=96777
- 0085: dt=2.880000, rms=0.705 (0.187%), neg=0, invalid=96777
- 0086: dt=2.880000, rms=0.705 (-0.047%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.705, neg=0, invalid=96777
- 0087: dt=0.000000, rms=0.705 (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=0.778, neg=0, invalid=96777
- 0088: dt=1.278926, rms=0.771 (0.800%), neg=0, invalid=96777
- 0089: dt=2.075117, rms=0.764 (0.918%), neg=0, invalid=96777
- 0090: dt=0.474138, rms=0.764 (0.108%), neg=0, invalid=96777
- 0091: dt=0.474138, rms=0.763 (0.037%), neg=0, invalid=96777
- 0092: dt=0.474138, rms=0.763 (0.032%), neg=0, invalid=96777
- 0093: dt=0.474138, rms=0.763 (0.001%), neg=0, invalid=96777
- 0094: dt=1.792000, rms=0.762 (0.137%), neg=0, invalid=96777
- 0095: dt=0.112000, rms=0.762 (0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.762, neg=0, invalid=96777
- 0096: dt=0.448000, rms=0.762 (0.047%), neg=0, invalid=96777
- 0097: dt=0.112000, rms=0.762 (-0.003%), 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=0.723, neg=0, invalid=96777
- 0098: dt=0.448000, rms=0.700 (3.088%), neg=0, invalid=96777
- 0099: dt=0.000000, rms=0.700 (0.006%), neg=0, invalid=96777
- 0100: dt=0.050000, rms=0.700 (-0.558%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.700, neg=0, invalid=96777
- 0101: dt=0.000000, rms=0.700 (0.000%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.13388 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (1805 voxels, overlap=0.006)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1805 voxels, peak = 7), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.11438 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (995 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (995 voxels, peak = 7), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.07713 (89)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (435 voxels, overlap=0.104)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (435 voxels, peak = 92), gca=91.5
- gca peak = 0.19192 (97)
- mri peak = 0.07113 (86)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (268 voxels, overlap=0.558)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (268 voxels, peak = 85), gca=84.9
- gca peak = 0.24007 (63)
- mri peak = 0.06438 (63)
- Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (548 voxels, overlap=0.725)
- Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (548 voxels, peak = 57), gca=57.0
- gca peak = 0.29892 (64)
- mri peak = 0.07181 (61)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (633 voxels, overlap=0.930)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (633 voxels, peak = 59), gca=59.2
- gca peak = 0.12541 (104)
- mri peak = 0.08267 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76042 voxels, overlap=0.760)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76042 voxels, peak = 108), gca=107.6
- gca peak = 0.13686 (104)
- mri peak = 0.08044 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (78479 voxels, overlap=0.713)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (78479 voxels, peak = 108), gca=107.6
- gca peak = 0.11691 (63)
- mri peak = 0.05104 (54)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (21575 voxels, overlap=0.379)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (21575 voxels, peak = 53), gca=53.2
- gca peak = 0.13270 (63)
- mri peak = 0.04791 (52)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (21648 voxels, overlap=0.382)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (21648 voxels, peak = 52), gca=52.0
- gca peak = 0.15182 (70)
- mri peak = 0.09658 (64)
- Right_Caudate (50): linear fit = 0.89 x + 0.0 (470 voxels, overlap=0.363)
- Right_Caudate (50): linear fit = 0.89 x + 0.0 (470 voxels, peak = 63), gca=62.6
- gca peak = 0.14251 (76)
- mri peak = 0.07769 (68)
- Left_Caudate (11): linear fit = 0.85 x + 0.0 (845 voxels, overlap=0.365)
- Left_Caudate (11): linear fit = 0.85 x + 0.0 (845 voxels, peak = 64), gca=64.2
- gca peak = 0.12116 (60)
- mri peak = 0.04100 (51)
- Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (13216 voxels, overlap=0.498)
- Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (13216 voxels, peak = 53), gca=53.1
- gca peak = 0.12723 (61)
- mri peak = 0.04605 (51)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (14246 voxels, overlap=0.732)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (14246 voxels, peak = 56), gca=55.8
- gca peak = 0.22684 (88)
- mri peak = 0.07191 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7317 voxels, overlap=0.904)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7317 voxels, peak = 91), gca=91.1
- gca peak = 0.21067 (87)
- mri peak = 0.07444 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6810 voxels, overlap=0.923)
- Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6810 voxels, peak = 89), gca=89.2
- gca peak = 0.25455 (62)
- mri peak = 0.09069 (63)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (413 voxels, overlap=0.999)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (413 voxels, peak = 62), gca=62.0
- gca peak = 0.39668 (62)
- mri peak = 0.08782 (54)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (364 voxels, overlap=0.997)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (364 voxels, peak = 54), gca=54.2
- gca peak = 0.10129 (93)
- mri peak = 0.05045 (95)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5858 voxels, overlap=0.987)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5858 voxels, peak = 94), gca=94.4
- gca peak = 0.12071 (89)
- mri peak = 0.05184 (87)
- Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (3750 voxels, overlap=0.972)
- Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (3750 voxels, peak = 86), gca=85.9
- gca peak = 0.13716 (82)
- mri peak = 0.05498 (79)
- Left_Putamen (12): linear fit = 0.95 x + 0.0 (2334 voxels, overlap=0.826)
- Left_Putamen (12): linear fit = 0.95 x + 0.0 (2334 voxels, peak = 78), gca=78.3
- gca peak = 0.15214 (84)
- mri peak = 0.04022 (73)
- Right_Putamen (51): linear fit = 0.86 x + 0.0 (2222 voxels, overlap=0.338)
- Right_Putamen (51): linear fit = 0.86 x + 0.0 (2222 voxels, peak = 72), gca=71.8
- gca peak = 0.08983 (85)
- mri peak = 0.06721 (86)
- Brain_Stem (16): linear fit = 1.04 x + 0.0 (11530 voxels, overlap=0.778)
- Brain_Stem (16): linear fit = 1.04 x + 0.0 (11530 voxels, peak = 89), gca=88.8
- gca peak = 0.11809 (92)
- mri peak = 0.07593 (94)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (814 voxels, overlap=0.681)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (814 voxels, peak = 94), gca=94.3
- gca peak = 0.12914 (94)
- mri peak = 0.06676 (94)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (982 voxels, overlap=0.802)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (982 voxels, peak = 95), gca=95.4
- gca peak = 0.21100 (36)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.13542 (27)
- mri peak = 0.11251 (10)
- Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (384 voxels, overlap=0.027)
- Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (384 voxels, peak = 10), gca=9.9
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- gca peak Third_Ventricle = 0.21100 (36)
- 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 0.90 x + 0.0
- estimating mean wm scale to be 1.03 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to 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=0.723, neg=0, invalid=96777
- 0102: dt=129.472000, rms=0.717 (0.854%), neg=0, invalid=96777
- 0103: dt=129.472000, rms=0.714 (0.329%), neg=0, invalid=96777
- 0104: dt=295.936000, rms=0.710 (0.512%), neg=0, invalid=96777
- 0105: dt=32.368000, rms=0.710 (0.107%), neg=0, invalid=96777
- 0106: dt=73.984000, rms=0.709 (0.062%), neg=0, invalid=96777
- 0107: dt=517.888000, rms=0.706 (0.399%), neg=0, invalid=96777
- 0108: dt=32.368000, rms=0.706 (0.113%), neg=0, invalid=96777
- 0109: dt=32.368000, rms=0.705 (0.034%), neg=0, invalid=96777
- 0110: dt=32.368000, rms=0.705 (0.021%), neg=0, invalid=96777
- 0111: dt=32.368000, rms=0.705 (0.029%), neg=0, invalid=96777
- 0112: dt=32.368000, rms=0.705 (0.045%), neg=0, invalid=96777
- 0113: dt=32.368000, rms=0.704 (0.072%), neg=0, invalid=96777
- 0114: dt=32.368000, rms=0.704 (0.088%), neg=0, invalid=96777
- 0115: dt=32.368000, rms=0.703 (0.100%), neg=0, invalid=96777
- 0116: dt=32.368000, rms=0.702 (0.096%), neg=0, invalid=96777
- 0117: dt=32.368000, rms=0.702 (0.096%), neg=0, invalid=96777
- 0118: dt=32.368000, rms=0.701 (0.093%), neg=0, invalid=96777
- 0119: dt=32.368000, rms=0.700 (0.088%), neg=0, invalid=96777
- 0120: dt=32.368000, rms=0.700 (0.087%), neg=0, invalid=96777
- 0121: dt=32.368000, rms=0.699 (0.087%), neg=0, invalid=96777
- 0122: dt=32.368000, rms=0.699 (0.083%), neg=0, invalid=96777
- 0123: dt=32.368000, rms=0.698 (0.076%), neg=0, invalid=96777
- 0124: dt=32.368000, rms=0.697 (0.074%), neg=0, invalid=96777
- 0125: dt=32.368000, rms=0.697 (0.073%), neg=0, invalid=96777
- 0126: dt=32.368000, rms=0.696 (0.074%), neg=0, invalid=96777
- 0127: dt=32.368000, rms=0.696 (0.070%), neg=0, invalid=96777
- 0128: dt=32.368000, rms=0.695 (0.068%), neg=0, invalid=96777
- 0129: dt=32.368000, rms=0.695 (0.066%), neg=0, invalid=96777
- 0130: dt=32.368000, rms=0.695 (0.061%), neg=0, invalid=96777
- 0131: dt=32.368000, rms=0.694 (0.064%), neg=0, invalid=96777
- 0132: dt=32.368000, rms=0.694 (0.056%), neg=0, invalid=96777
- 0133: dt=32.368000, rms=0.693 (0.056%), neg=0, invalid=96777
- 0134: dt=32.368000, rms=0.693 (0.048%), neg=0, invalid=96777
- 0135: dt=32.368000, rms=0.693 (0.046%), neg=0, invalid=96777
- 0136: dt=32.368000, rms=0.692 (0.053%), neg=0, invalid=96777
- 0137: dt=32.368000, rms=0.692 (0.055%), neg=0, invalid=96777
- 0138: dt=32.368000, rms=0.692 (0.054%), neg=0, invalid=96777
- 0139: dt=32.368000, rms=0.691 (0.049%), neg=0, invalid=96777
- 0140: dt=32.368000, rms=0.691 (0.045%), neg=0, invalid=96777
- 0141: dt=32.368000, rms=0.691 (0.041%), neg=0, invalid=96777
- 0142: dt=32.368000, rms=0.690 (0.040%), neg=0, invalid=96777
- 0143: dt=32.368000, rms=0.690 (0.038%), neg=0, invalid=96777
- 0144: dt=32.368000, rms=0.690 (0.042%), neg=0, invalid=96777
- 0145: dt=32.368000, rms=0.690 (0.043%), neg=0, invalid=96777
- 0146: dt=32.368000, rms=0.689 (0.043%), neg=0, invalid=96777
- 0147: dt=32.368000, rms=0.689 (0.042%), neg=0, invalid=96777
- 0148: dt=32.368000, rms=0.689 (0.041%), neg=0, invalid=96777
- 0149: dt=32.368000, rms=0.688 (0.036%), neg=0, invalid=96777
- 0150: dt=32.368000, rms=0.688 (0.034%), neg=0, invalid=96777
- 0151: dt=32.368000, rms=0.688 (0.036%), neg=0, invalid=96777
- 0152: dt=32.368000, rms=0.688 (0.033%), neg=0, invalid=96777
- 0153: dt=32.368000, rms=0.687 (0.031%), neg=0, invalid=96777
- 0154: dt=32.368000, rms=0.687 (0.029%), neg=0, invalid=96777
- 0155: dt=32.368000, rms=0.687 (0.029%), neg=0, invalid=96777
- 0156: dt=32.368000, rms=0.687 (0.030%), neg=0, invalid=96777
- 0157: dt=32.368000, rms=0.687 (0.030%), neg=0, invalid=96777
- 0158: dt=32.368000, rms=0.686 (0.030%), neg=0, invalid=96777
- 0159: dt=32.368000, rms=0.686 (0.028%), neg=0, invalid=96777
- 0160: dt=32.368000, rms=0.686 (0.029%), neg=0, invalid=96777
- 0161: dt=32.368000, rms=0.686 (0.029%), neg=0, invalid=96777
- 0162: dt=32.368000, rms=0.686 (0.027%), neg=0, invalid=96777
- 0163: dt=32.368000, rms=0.686 (0.025%), neg=0, invalid=96777
- 0164: dt=32.368000, rms=0.685 (0.028%), neg=0, invalid=96777
- 0165: dt=32.368000, rms=0.685 (0.027%), neg=0, invalid=96777
- 0166: dt=32.368000, rms=0.685 (0.027%), neg=0, invalid=96777
- 0167: dt=32.368000, rms=0.685 (0.026%), neg=0, invalid=96777
- 0168: dt=32.368000, rms=0.685 (0.026%), neg=0, invalid=96777
- 0169: dt=32.368000, rms=0.684 (0.025%), neg=0, invalid=96777
- 0170: dt=32.368000, rms=0.684 (0.025%), neg=0, invalid=96777
- 0171: dt=129.472000, rms=0.684 (0.001%), neg=0, invalid=96777
- 0172: dt=129.472000, rms=0.684 (0.021%), neg=0, invalid=96777
- 0173: dt=129.472000, rms=0.684 (0.013%), neg=0, invalid=96777
- 0174: dt=129.472000, rms=0.684 (0.016%), neg=0, invalid=96777
- 0175: dt=129.472000, rms=0.684 (0.031%), neg=0, invalid=96777
- 0176: dt=129.472000, rms=0.683 (0.043%), neg=0, invalid=96777
- 0177: dt=129.472000, rms=0.683 (0.036%), neg=0, invalid=96777
- 0178: dt=129.472000, rms=0.683 (0.030%), neg=0, invalid=96777
- 0179: dt=129.472000, rms=0.683 (0.065%), neg=0, invalid=96777
- 0180: dt=129.472000, rms=0.682 (0.052%), neg=0, invalid=96777
- 0181: dt=129.472000, rms=0.682 (0.032%), neg=0, invalid=96777
- 0182: dt=129.472000, rms=0.682 (0.055%), neg=0, invalid=96777
- 0183: dt=129.472000, rms=0.681 (0.049%), neg=0, invalid=96777
- 0184: dt=129.472000, rms=0.681 (0.038%), neg=0, invalid=96777
- 0185: dt=129.472000, rms=0.681 (0.057%), neg=0, invalid=96777
- 0186: dt=129.472000, rms=0.680 (0.049%), neg=0, invalid=96777
- 0187: dt=129.472000, rms=0.680 (0.044%), neg=0, invalid=96777
- 0188: dt=129.472000, rms=0.680 (0.048%), neg=0, invalid=96777
- 0189: dt=129.472000, rms=0.679 (0.048%), neg=0, invalid=96777
- 0190: dt=129.472000, rms=0.679 (0.039%), neg=0, invalid=96777
- 0191: dt=129.472000, rms=0.679 (0.033%), neg=0, invalid=96777
- 0192: dt=129.472000, rms=0.678 (0.050%), neg=0, invalid=96777
- 0193: dt=129.472000, rms=0.678 (0.040%), neg=0, invalid=96777
- 0194: dt=129.472000, rms=0.678 (0.033%), neg=0, invalid=96777
- 0195: dt=129.472000, rms=0.678 (0.038%), neg=0, invalid=96777
- 0196: dt=129.472000, rms=0.677 (0.035%), neg=0, invalid=96777
- 0197: dt=129.472000, rms=0.677 (0.042%), neg=0, invalid=96777
- 0198: dt=129.472000, rms=0.677 (0.036%), neg=0, invalid=96777
- 0199: dt=129.472000, rms=0.677 (0.032%), neg=0, invalid=96777
- 0200: dt=129.472000, rms=0.676 (0.050%), neg=0, invalid=96777
- 0201: dt=129.472000, rms=0.676 (0.029%), neg=0, invalid=96777
- 0202: dt=129.472000, rms=0.676 (0.026%), neg=0, invalid=96777
- 0203: dt=129.472000, rms=0.676 (0.037%), neg=0, invalid=96777
- 0204: dt=129.472000, rms=0.676 (0.023%), neg=0, invalid=96777
- 0205: dt=129.472000, rms=0.675 (0.028%), neg=0, invalid=96777
- 0206: dt=129.472000, rms=0.675 (0.035%), neg=0, invalid=96777
- 0207: dt=129.472000, rms=0.675 (0.031%), neg=0, invalid=96777
- 0208: dt=129.472000, rms=0.675 (0.024%), neg=0, invalid=96777
- 0209: dt=129.472000, rms=0.675 (0.033%), neg=0, invalid=96777
- 0210: dt=129.472000, rms=0.674 (0.032%), neg=0, invalid=96777
- 0211: dt=129.472000, rms=0.674 (0.021%), neg=0, invalid=96777
- 0212: dt=129.472000, rms=0.674 (0.022%), neg=0, invalid=96777
- 0213: dt=129.472000, rms=0.674 (0.032%), neg=0, invalid=96777
- 0214: dt=129.472000, rms=0.674 (0.030%), neg=0, invalid=96777
- 0215: dt=129.472000, rms=0.674 (0.019%), neg=0, invalid=96777
- 0216: dt=129.472000, rms=0.673 (0.015%), neg=0, invalid=96777
- 0217: dt=295.936000, rms=0.673 (0.025%), neg=0, invalid=96777
- 0218: dt=6.936000, rms=0.673 (0.002%), neg=0, invalid=96777
- 0219: dt=6.936000, rms=0.673 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.673, neg=0, invalid=96777
- 0220: dt=73.984000, rms=0.673 (0.041%), neg=0, invalid=96777
- 0221: dt=369.920000, rms=0.672 (0.146%), neg=0, invalid=96777
- 0222: dt=6.936000, rms=0.672 (0.003%), neg=0, invalid=96777
- 0223: dt=6.936000, rms=0.672 (-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=0.673, neg=0, invalid=96777
- 0224: dt=103.680000, rms=0.669 (0.598%), neg=0, invalid=96777
- 0225: dt=62.208000, rms=0.664 (0.693%), neg=0, invalid=96777
- 0226: dt=15.552000, rms=0.663 (0.204%), neg=0, invalid=96777
- 0227: dt=124.416000, rms=0.661 (0.329%), neg=0, invalid=96777
- 0228: dt=31.104000, rms=0.656 (0.676%), neg=0, invalid=96777
- 0229: dt=25.920000, rms=0.656 (0.073%), neg=0, invalid=96777
- 0230: dt=145.152000, rms=0.652 (0.595%), neg=0, invalid=96777
- 0231: dt=15.552000, rms=0.650 (0.244%), neg=0, invalid=96777
- 0232: dt=36.288000, rms=0.650 (0.086%), neg=0, invalid=96777
- 0233: dt=82.944000, rms=0.648 (0.361%), neg=0, invalid=96777
- 0234: dt=9.072000, rms=0.647 (0.092%), neg=0, invalid=96777
- 0235: dt=9.072000, rms=0.647 (0.038%), neg=0, invalid=96777
- 0236: dt=9.072000, rms=0.647 (0.030%), neg=0, invalid=96777
- 0237: dt=9.072000, rms=0.646 (0.043%), neg=0, invalid=96777
- 0238: dt=9.072000, rms=0.646 (0.070%), neg=0, invalid=96777
- 0239: dt=9.072000, rms=0.645 (0.100%), neg=0, invalid=96777
- 0240: dt=9.072000, rms=0.644 (0.136%), neg=0, invalid=96777
- 0241: dt=9.072000, rms=0.643 (0.165%), neg=0, invalid=96777
- 0242: dt=9.072000, rms=0.642 (0.173%), neg=0, invalid=96777
- 0243: dt=9.072000, rms=0.641 (0.171%), neg=0, invalid=96777
- 0244: dt=9.072000, rms=0.640 (0.169%), neg=0, invalid=96777
- 0245: dt=9.072000, rms=0.639 (0.165%), neg=0, invalid=96777
- 0246: dt=9.072000, rms=0.638 (0.161%), neg=0, invalid=96777
- 0247: dt=9.072000, rms=0.637 (0.160%), neg=0, invalid=96777
- 0248: dt=9.072000, rms=0.636 (0.161%), neg=0, invalid=96777
- 0249: dt=9.072000, rms=0.635 (0.173%), neg=0, invalid=96777
- 0250: dt=9.072000, rms=0.634 (0.170%), neg=0, invalid=96777
- 0251: dt=9.072000, rms=0.633 (0.164%), neg=0, invalid=96777
- 0252: dt=9.072000, rms=0.632 (0.161%), neg=0, invalid=96777
- 0253: dt=9.072000, rms=0.631 (0.150%), neg=0, invalid=96777
- 0254: dt=9.072000, rms=0.630 (0.146%), neg=0, invalid=96777
- 0255: dt=9.072000, rms=0.629 (0.139%), neg=0, invalid=96777
- 0256: dt=9.072000, rms=0.628 (0.136%), neg=0, invalid=96777
- 0257: dt=9.072000, rms=0.627 (0.135%), neg=0, invalid=96777
- 0258: dt=9.072000, rms=0.626 (0.139%), neg=0, invalid=96777
- 0259: dt=9.072000, rms=0.625 (0.133%), neg=0, invalid=96777
- 0260: dt=9.072000, rms=0.625 (0.137%), neg=0, invalid=96777
- 0261: dt=9.072000, rms=0.624 (0.128%), neg=0, invalid=96777
- 0262: dt=9.072000, rms=0.623 (0.127%), neg=0, invalid=96777
- 0263: dt=9.072000, rms=0.622 (0.123%), neg=0, invalid=96777
- 0264: dt=9.072000, rms=0.621 (0.121%), neg=0, invalid=96777
- 0265: dt=9.072000, rms=0.621 (0.118%), neg=0, invalid=96777
- 0266: dt=9.072000, rms=0.620 (0.116%), neg=0, invalid=96777
- 0267: dt=9.072000, rms=0.619 (0.109%), neg=0, invalid=96777
- 0268: dt=9.072000, rms=0.619 (0.110%), neg=0, invalid=96777
- 0269: dt=9.072000, rms=0.618 (0.103%), neg=0, invalid=96777
- 0270: dt=9.072000, rms=0.617 (0.094%), neg=0, invalid=96777
- 0271: dt=9.072000, rms=0.617 (0.088%), neg=0, invalid=96777
- 0272: dt=9.072000, rms=0.616 (0.088%), neg=0, invalid=96777
- 0273: dt=9.072000, rms=0.616 (0.084%), neg=0, invalid=96777
- 0274: dt=9.072000, rms=0.615 (0.089%), neg=0, invalid=96777
- 0275: dt=9.072000, rms=0.615 (0.089%), neg=0, invalid=96777
- 0276: dt=9.072000, rms=0.614 (0.080%), neg=0, invalid=96777
- 0277: dt=9.072000, rms=0.614 (0.082%), neg=0, invalid=96777
- 0278: dt=9.072000, rms=0.613 (0.078%), neg=0, invalid=96777
- 0279: dt=9.072000, rms=0.613 (0.076%), neg=0, invalid=96777
- 0280: dt=9.072000, rms=0.612 (0.072%), neg=0, invalid=96777
- 0281: dt=9.072000, rms=0.612 (0.071%), neg=0, invalid=96777
- 0282: dt=9.072000, rms=0.611 (0.068%), neg=0, invalid=96777
- 0283: dt=9.072000, rms=0.611 (0.067%), neg=0, invalid=96777
- 0284: dt=9.072000, rms=0.611 (0.064%), neg=0, invalid=96777
- 0285: dt=9.072000, rms=0.610 (0.061%), neg=0, invalid=96777
- 0286: dt=9.072000, rms=0.610 (0.061%), neg=0, invalid=96777
- 0287: dt=9.072000, rms=0.610 (0.059%), neg=0, invalid=96777
- 0288: dt=9.072000, rms=0.609 (0.059%), neg=0, invalid=96777
- 0289: dt=9.072000, rms=0.609 (0.058%), neg=0, invalid=96777
- 0290: dt=9.072000, rms=0.609 (0.055%), neg=0, invalid=96777
- 0291: dt=9.072000, rms=0.608 (0.049%), neg=0, invalid=96777
- 0292: dt=9.072000, rms=0.608 (0.053%), neg=0, invalid=96777
- 0293: dt=9.072000, rms=0.608 (0.052%), neg=0, invalid=96777
- 0294: dt=9.072000, rms=0.607 (0.053%), neg=0, invalid=96777
- 0295: dt=9.072000, rms=0.607 (0.050%), neg=0, invalid=96777
- 0296: dt=9.072000, rms=0.607 (0.048%), neg=0, invalid=96777
- 0297: dt=9.072000, rms=0.606 (0.045%), neg=0, invalid=96777
- 0298: dt=9.072000, rms=0.606 (0.045%), neg=0, invalid=96777
- 0299: dt=9.072000, rms=0.606 (0.046%), neg=0, invalid=96777
- 0300: dt=9.072000, rms=0.606 (0.043%), neg=0, invalid=96777
- 0301: dt=9.072000, rms=0.605 (0.043%), neg=0, invalid=96777
- 0302: dt=9.072000, rms=0.605 (0.045%), neg=0, invalid=96777
- 0303: dt=9.072000, rms=0.605 (0.049%), neg=0, invalid=96777
- 0304: dt=9.072000, rms=0.604 (0.045%), neg=0, invalid=96777
- 0305: dt=9.072000, rms=0.604 (0.043%), neg=0, invalid=96777
- 0306: dt=9.072000, rms=0.604 (0.042%), neg=0, invalid=96777
- 0307: dt=9.072000, rms=0.604 (0.043%), neg=0, invalid=96777
- 0308: dt=9.072000, rms=0.603 (0.039%), neg=0, invalid=96777
- 0309: dt=9.072000, rms=0.603 (0.034%), neg=0, invalid=96777
- 0310: dt=9.072000, rms=0.603 (0.035%), neg=0, invalid=96777
- 0311: dt=9.072000, rms=0.603 (0.029%), neg=0, invalid=96777
- 0312: dt=9.072000, rms=0.603 (0.034%), neg=0, invalid=96777
- 0313: dt=9.072000, rms=0.602 (0.040%), neg=0, invalid=96777
- 0314: dt=9.072000, rms=0.602 (0.040%), neg=0, invalid=96777
- 0315: dt=9.072000, rms=0.602 (0.040%), neg=0, invalid=96777
- 0316: dt=9.072000, rms=0.602 (0.042%), neg=0, invalid=96777
- 0317: dt=9.072000, rms=0.602 (0.032%), neg=0, invalid=96777
- 0318: dt=9.072000, rms=0.601 (0.036%), neg=0, invalid=96777
- 0319: dt=9.072000, rms=0.601 (0.027%), neg=0, invalid=96777
- 0320: dt=9.072000, rms=0.601 (0.034%), neg=0, invalid=96777
- 0321: dt=9.072000, rms=0.601 (0.037%), neg=0, invalid=96777
- 0322: dt=9.072000, rms=0.600 (0.039%), neg=0, invalid=96777
- 0323: dt=9.072000, rms=0.600 (0.039%), neg=0, invalid=96777
- 0324: dt=9.072000, rms=0.600 (0.035%), neg=0, invalid=96777
- 0325: dt=9.072000, rms=0.600 (0.033%), neg=0, invalid=96777
- 0326: dt=9.072000, rms=0.600 (0.036%), neg=0, invalid=96777
- 0327: dt=9.072000, rms=0.599 (0.031%), neg=0, invalid=96777
- 0328: dt=9.072000, rms=0.599 (0.027%), neg=0, invalid=96777
- 0329: dt=9.072000, rms=0.599 (0.032%), neg=0, invalid=96777
- 0330: dt=9.072000, rms=0.599 (0.034%), neg=0, invalid=96777
- 0331: dt=9.072000, rms=0.599 (0.031%), neg=0, invalid=96777
- 0332: dt=9.072000, rms=0.599 (0.032%), neg=0, invalid=96777
- 0333: dt=9.072000, rms=0.598 (0.035%), neg=0, invalid=96777
- 0334: dt=9.072000, rms=0.598 (0.032%), neg=0, invalid=96777
- 0335: dt=9.072000, rms=0.598 (0.031%), neg=0, invalid=96777
- 0336: dt=9.072000, rms=0.598 (0.029%), neg=0, invalid=96777
- 0337: dt=9.072000, rms=0.598 (0.030%), neg=0, invalid=96777
- 0338: dt=9.072000, rms=0.597 (0.028%), neg=0, invalid=96777
- 0339: dt=9.072000, rms=0.597 (0.034%), neg=0, invalid=96777
- 0340: dt=9.072000, rms=0.597 (0.026%), neg=0, invalid=96777
- 0341: dt=9.072000, rms=0.597 (0.027%), neg=0, invalid=96777
- 0342: dt=9.072000, rms=0.597 (0.024%), neg=0, invalid=96777
- 0343: dt=9.072000, rms=0.597 (0.023%), neg=0, invalid=96777
- 0344: dt=580.608000, rms=0.596 (0.112%), neg=0, invalid=96777
- 0345: dt=15.552000, rms=0.596 (0.036%), neg=0, invalid=96777
- 0346: dt=15.552000, rms=0.596 (0.007%), neg=0, invalid=96777
- 0347: dt=15.552000, rms=0.596 (-0.008%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.596, neg=0, invalid=96777
- 0348: dt=82.944000, rms=0.594 (0.219%), neg=0, invalid=96777
- 0349: dt=36.288000, rms=0.594 (0.140%), neg=0, invalid=96777
- 0350: dt=103.680000, rms=0.593 (0.069%), neg=0, invalid=96777
- 0351: dt=36.288000, rms=0.593 (0.092%), neg=0, invalid=96777
- 0352: dt=36.288000, rms=0.592 (0.037%), neg=0, invalid=96777
- 0353: dt=36.288000, rms=0.592 (0.046%), neg=0, invalid=96777
- 0354: dt=36.288000, rms=0.592 (0.038%), neg=0, invalid=96777
- 0355: dt=36.288000, rms=0.592 (0.050%), neg=0, invalid=96777
- 0356: dt=36.288000, rms=0.591 (0.072%), neg=0, invalid=96777
- 0357: dt=36.288000, rms=0.591 (0.087%), neg=0, invalid=96777
- 0358: dt=36.288000, rms=0.590 (0.081%), neg=0, invalid=96777
- 0359: dt=36.288000, rms=0.590 (0.065%), neg=0, invalid=96777
- 0360: dt=36.288000, rms=0.589 (0.066%), neg=0, invalid=96777
- 0361: dt=36.288000, rms=0.589 (0.070%), neg=0, invalid=96777
- 0362: dt=36.288000, rms=0.589 (0.068%), neg=0, invalid=96777
- 0363: dt=36.288000, rms=0.588 (0.068%), neg=0, invalid=96777
- 0364: dt=36.288000, rms=0.588 (0.067%), neg=0, invalid=96777
- 0365: dt=36.288000, rms=0.587 (0.074%), neg=0, invalid=96777
- 0366: dt=36.288000, rms=0.587 (0.073%), neg=0, invalid=96777
- 0367: dt=36.288000, rms=0.586 (0.079%), neg=0, invalid=96777
- 0368: dt=36.288000, rms=0.586 (0.078%), neg=0, invalid=96777
- 0369: dt=36.288000, rms=0.586 (0.065%), neg=0, invalid=96777
- 0370: dt=36.288000, rms=0.585 (0.067%), neg=0, invalid=96777
- 0371: dt=36.288000, rms=0.585 (0.057%), neg=0, invalid=96777
- 0372: dt=36.288000, rms=0.585 (0.054%), neg=0, invalid=96777
- 0373: dt=36.288000, rms=0.584 (0.073%), neg=0, invalid=96777
- 0374: dt=36.288000, rms=0.584 (0.064%), neg=0, invalid=96777
- 0375: dt=36.288000, rms=0.583 (0.058%), neg=0, invalid=96777
- 0376: dt=36.288000, rms=0.583 (0.059%), neg=0, invalid=96777
- 0377: dt=36.288000, rms=0.583 (0.054%), neg=0, invalid=96777
- 0378: dt=36.288000, rms=0.582 (0.047%), neg=0, invalid=96777
- 0379: dt=36.288000, rms=0.582 (0.049%), neg=0, invalid=96777
- 0380: dt=36.288000, rms=0.582 (0.052%), neg=0, invalid=96777
- 0381: dt=36.288000, rms=0.582 (0.061%), neg=0, invalid=96777
- 0382: dt=36.288000, rms=0.581 (0.055%), neg=0, invalid=96777
- 0383: dt=36.288000, rms=0.581 (0.047%), neg=0, invalid=96777
- 0384: dt=36.288000, rms=0.581 (0.047%), neg=0, invalid=96777
- 0385: dt=36.288000, rms=0.580 (0.046%), neg=0, invalid=96777
- 0386: dt=36.288000, rms=0.580 (0.050%), neg=0, invalid=96777
- 0387: dt=36.288000, rms=0.580 (0.062%), neg=0, invalid=96777
- 0388: dt=36.288000, rms=0.579 (0.054%), neg=0, invalid=96777
- 0389: dt=36.288000, rms=0.579 (0.046%), neg=0, invalid=96777
- 0390: dt=36.288000, rms=0.579 (0.047%), neg=0, invalid=96777
- 0391: dt=36.288000, rms=0.579 (0.040%), neg=0, invalid=96777
- 0392: dt=36.288000, rms=0.578 (0.043%), neg=0, invalid=96777
- 0393: dt=36.288000, rms=0.578 (0.040%), neg=0, invalid=96777
- 0394: dt=36.288000, rms=0.578 (0.036%), neg=0, invalid=96777
- 0395: dt=36.288000, rms=0.578 (0.037%), neg=0, invalid=96777
- 0396: dt=36.288000, rms=0.578 (0.036%), neg=0, invalid=96777
- 0397: dt=36.288000, rms=0.577 (0.035%), neg=0, invalid=96777
- 0398: dt=36.288000, rms=0.577 (0.031%), neg=0, invalid=96777
- 0399: dt=36.288000, rms=0.577 (0.027%), neg=0, invalid=96777
- 0400: dt=36.288000, rms=0.577 (0.023%), neg=0, invalid=96777
- 0401: dt=36.288000, rms=0.577 (0.024%), neg=0, invalid=96777
- 0402: dt=36.288000, rms=0.577 (0.030%), neg=0, invalid=96777
- 0403: dt=36.288000, rms=0.576 (0.034%), neg=0, invalid=96777
- 0404: dt=36.288000, rms=0.576 (0.032%), neg=0, invalid=96777
- 0405: dt=36.288000, rms=0.576 (0.025%), neg=0, invalid=96777
- 0406: dt=36.288000, rms=0.576 (0.021%), neg=0, invalid=96777
- 0407: dt=36.288000, rms=0.576 (0.026%), neg=0, invalid=96777
- 0408: dt=36.288000, rms=0.576 (0.030%), neg=0, invalid=96777
- 0409: dt=36.288000, rms=0.575 (0.026%), neg=0, invalid=96777
- 0410: dt=36.288000, rms=0.575 (0.020%), neg=0, invalid=96777
- 0411: dt=36.288000, rms=0.575 (0.026%), neg=0, invalid=96777
- 0412: dt=36.288000, rms=0.575 (0.016%), neg=0, invalid=96777
- 0413: dt=36.288000, rms=0.575 (0.030%), neg=0, invalid=96777
- 0414: dt=36.288000, rms=0.575 (0.031%), neg=0, invalid=96777
- 0415: dt=36.288000, rms=0.575 (0.033%), neg=0, invalid=96777
- 0416: dt=36.288000, rms=0.574 (0.027%), neg=0, invalid=96777
- 0417: dt=36.288000, rms=0.574 (0.027%), neg=0, invalid=96777
- 0418: dt=36.288000, rms=0.574 (0.019%), neg=0, invalid=96777
- 0419: dt=36.288000, rms=0.574 (0.012%), neg=0, invalid=96777
- 0420: dt=103.680000, rms=0.574 (0.012%), neg=0, invalid=96777
- 0421: dt=103.680000, rms=0.574 (-0.060%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.582, neg=0, invalid=96777
- 0422: dt=25.600000, rms=0.580 (0.293%), neg=0, invalid=96777
- 0423: dt=38.400000, rms=0.578 (0.316%), neg=0, invalid=96777
- 0424: dt=5.908497, rms=0.578 (0.119%), neg=0, invalid=96777
- 0425: dt=44.800000, rms=0.575 (0.508%), neg=0, invalid=96777
- 0426: dt=8.000000, rms=0.574 (0.079%), neg=0, invalid=96777
- 0427: dt=44.800000, rms=0.571 (0.493%), neg=0, invalid=96777
- 0428: dt=6.400000, rms=0.571 (0.041%), neg=0, invalid=96777
- 0429: dt=6.400000, rms=0.571 (0.088%), neg=0, invalid=96777
- 0430: dt=6.400000, rms=0.570 (0.130%), neg=0, invalid=96777
- 0431: dt=6.400000, rms=0.569 (0.158%), neg=0, invalid=96777
- 0432: dt=6.400000, rms=0.568 (0.185%), neg=0, invalid=96777
- 0433: dt=6.400000, rms=0.567 (0.191%), neg=0, invalid=96777
- 0434: dt=6.400000, rms=0.565 (0.244%), neg=0, invalid=96777
- 0435: dt=6.400000, rms=0.564 (0.285%), neg=0, invalid=96777
- 0436: dt=6.400000, rms=0.562 (0.292%), neg=0, invalid=96777
- 0437: dt=6.400000, rms=0.561 (0.279%), neg=0, invalid=96777
- 0438: dt=6.400000, rms=0.559 (0.265%), neg=0, invalid=96777
- 0439: dt=6.400000, rms=0.558 (0.249%), neg=0, invalid=96777
- 0440: dt=6.400000, rms=0.556 (0.264%), neg=0, invalid=96777
- 0441: dt=6.400000, rms=0.555 (0.249%), neg=0, invalid=96777
- 0442: dt=6.400000, rms=0.553 (0.246%), neg=0, invalid=96777
- 0443: dt=6.400000, rms=0.552 (0.238%), neg=0, invalid=96777
- 0444: dt=6.400000, rms=0.551 (0.222%), neg=0, invalid=96777
- 0445: dt=6.400000, rms=0.550 (0.216%), neg=0, invalid=96777
- 0446: dt=6.400000, rms=0.549 (0.202%), neg=0, invalid=96777
- 0447: dt=6.400000, rms=0.548 (0.195%), neg=0, invalid=96777
- 0448: dt=6.400000, rms=0.547 (0.177%), neg=0, invalid=96777
- 0449: dt=6.400000, rms=0.546 (0.165%), neg=0, invalid=96777
- 0450: dt=6.400000, rms=0.545 (0.151%), neg=0, invalid=96777
- 0451: dt=6.400000, rms=0.544 (0.145%), neg=0, invalid=96777
- 0452: dt=6.400000, rms=0.543 (0.139%), neg=0, invalid=96777
- 0453: dt=6.400000, rms=0.543 (0.143%), neg=0, invalid=96777
- 0454: dt=6.400000, rms=0.542 (0.124%), neg=0, invalid=96777
- 0455: dt=6.400000, rms=0.541 (0.112%), neg=0, invalid=96777
- 0456: dt=6.400000, rms=0.541 (0.110%), neg=0, invalid=96777
- 0457: dt=6.400000, rms=0.540 (0.097%), neg=0, invalid=96777
- 0458: dt=6.400000, rms=0.540 (0.088%), neg=0, invalid=96777
- 0459: dt=6.400000, rms=0.539 (0.086%), neg=0, invalid=96777
- 0460: dt=6.400000, rms=0.539 (0.080%), neg=0, invalid=96777
- 0461: dt=6.400000, rms=0.538 (0.074%), neg=0, invalid=96777
- 0462: dt=6.400000, rms=0.538 (0.071%), neg=0, invalid=96777
- 0463: dt=6.400000, rms=0.538 (0.060%), neg=0, invalid=96777
- 0464: dt=6.400000, rms=0.537 (0.055%), neg=0, invalid=96777
- 0465: dt=6.400000, rms=0.537 (0.053%), neg=0, invalid=96777
- 0466: dt=6.400000, rms=0.537 (0.047%), neg=0, invalid=96777
- 0467: dt=6.400000, rms=0.537 (0.045%), neg=0, invalid=96777
- 0468: dt=6.400000, rms=0.536 (0.044%), neg=0, invalid=96777
- 0469: dt=6.400000, rms=0.536 (0.044%), neg=0, invalid=96777
- 0470: dt=6.400000, rms=0.536 (0.046%), neg=0, invalid=96777
- 0471: dt=6.400000, rms=0.536 (0.046%), neg=0, invalid=96777
- 0472: dt=6.400000, rms=0.535 (0.047%), neg=0, invalid=96777
- 0473: dt=6.400000, rms=0.535 (0.045%), neg=0, invalid=96777
- 0474: dt=6.400000, rms=0.535 (0.040%), neg=0, invalid=96777
- 0475: dt=6.400000, rms=0.535 (0.038%), neg=0, invalid=96777
- 0476: dt=6.400000, rms=0.535 (0.040%), neg=0, invalid=96777
- 0477: dt=6.400000, rms=0.534 (0.043%), neg=0, invalid=96777
- 0478: dt=6.400000, rms=0.534 (0.039%), neg=0, invalid=96777
- 0479: dt=6.400000, rms=0.534 (0.035%), neg=0, invalid=96777
- 0480: dt=6.400000, rms=0.534 (0.038%), neg=0, invalid=96777
- 0481: dt=6.400000, rms=0.533 (0.036%), neg=0, invalid=96777
- 0482: dt=6.400000, rms=0.533 (0.039%), neg=0, invalid=96777
- 0483: dt=6.400000, rms=0.533 (0.039%), neg=0, invalid=96777
- 0484: dt=6.400000, rms=0.533 (0.032%), neg=0, invalid=96777
- 0485: dt=6.400000, rms=0.533 (0.032%), neg=0, invalid=96777
- 0486: dt=6.400000, rms=0.533 (0.032%), neg=0, invalid=96777
- 0487: dt=6.400000, rms=0.532 (0.023%), neg=0, invalid=96777
- 0488: dt=6.400000, rms=0.532 (0.029%), neg=0, invalid=96777
- 0489: dt=6.400000, rms=0.532 (0.033%), neg=0, invalid=96777
- 0490: dt=6.400000, rms=0.532 (0.029%), neg=0, invalid=96777
- 0491: dt=6.400000, rms=0.532 (0.023%), neg=0, invalid=96777
- 0492: dt=6.400000, rms=0.532 (0.026%), neg=0, invalid=96777
- 0493: dt=6.400000, rms=0.532 (0.027%), neg=0, invalid=96777
- 0494: dt=6.400000, rms=0.531 (0.031%), neg=0, invalid=96777
- 0495: dt=6.400000, rms=0.531 (0.023%), neg=0, invalid=96777
- 0496: dt=6.400000, rms=0.531 (0.026%), neg=0, invalid=96777
- 0497: dt=6.400000, rms=0.531 (0.023%), neg=0, invalid=96777
- 0498: dt=6.400000, rms=0.531 (0.029%), neg=0, invalid=96777
- 0499: dt=6.400000, rms=0.531 (0.022%), neg=0, invalid=96777
- 0500: dt=6.400000, rms=0.531 (0.012%), neg=0, invalid=96777
- 0501: dt=9.600000, rms=0.531 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.531, neg=0, invalid=96777
- 0502: dt=38.400000, rms=0.529 (0.297%), neg=0, invalid=96777
- 0503: dt=9.600000, rms=0.529 (0.033%), neg=0, invalid=96777
- 0504: dt=9.600000, rms=0.529 (0.035%), neg=0, invalid=96777
- 0505: dt=9.600000, rms=0.529 (0.024%), neg=0, invalid=96777
- 0506: dt=9.600000, rms=0.529 (0.018%), neg=0, invalid=96777
- 0507: dt=32.000000, rms=0.528 (0.015%), neg=0, invalid=96777
- 0508: dt=32.000000, rms=0.528 (0.026%), neg=0, invalid=96777
- 0509: dt=32.000000, rms=0.528 (-0.195%), neg=0, invalid=96777
- 0510: dt=2.800000, rms=0.528 (0.013%), neg=0, invalid=96777
- 0511: dt=2.800000, rms=0.528 (0.013%), neg=0, invalid=96777
- 0512: dt=4.800000, rms=0.528 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.552, neg=0, invalid=96777
- 0513: dt=0.000000, rms=0.552 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.552, neg=0, invalid=96777
- 0514: dt=0.000000, rms=0.552 (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=0.599, neg=0, invalid=96777
- 0515: dt=1.402235, rms=0.593 (0.917%), neg=0, invalid=96777
- 0516: dt=0.384000, rms=0.593 (0.030%), neg=0, invalid=96777
- 0517: dt=0.384000, rms=0.593 (-0.017%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.593, neg=0, invalid=96777
- 0518: dt=0.571429, rms=0.592 (0.093%), neg=0, invalid=96777
- 0519: dt=0.320000, rms=0.592 (0.013%), neg=0, invalid=96777
- 0520: dt=0.320000, rms=0.592 (-0.009%), 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=0.545, neg=0, invalid=96777
- 0521: dt=0.174000, rms=0.537 (1.457%), neg=0, invalid=96777
- 0522: dt=0.142276, rms=0.532 (0.800%), neg=0, invalid=96777
- 0523: dt=0.448000, rms=0.523 (1.861%), neg=0, invalid=96777
- 0524: dt=0.028000, rms=0.522 (0.028%), neg=0, invalid=96777
- 0525: dt=0.028000, rms=0.522 (0.028%), neg=0, invalid=96777
- 0526: dt=0.028000, rms=0.522 (0.057%), neg=0, invalid=96777
- 0527: dt=0.028000, rms=0.522 (0.077%), neg=0, invalid=96777
- 0528: dt=0.028000, rms=0.521 (0.096%), neg=0, invalid=96777
- 0529: dt=0.028000, rms=0.520 (0.107%), neg=0, invalid=96777
- 0530: dt=0.028000, rms=0.520 (0.023%), neg=0, invalid=96777
- 0531: dt=0.028000, rms=0.520 (0.040%), neg=0, invalid=96777
- 0532: dt=0.028000, rms=0.520 (0.056%), neg=0, invalid=96777
- 0533: dt=0.028000, rms=0.519 (0.071%), neg=0, invalid=96777
- 0534: dt=0.028000, rms=0.519 (0.077%), neg=0, invalid=96777
- 0535: dt=0.028000, rms=0.519 (0.093%), neg=0, invalid=96777
- 0536: dt=0.028000, rms=0.518 (0.097%), neg=0, invalid=96777
- 0537: dt=0.028000, rms=0.518 (0.096%), neg=0, invalid=96777
- 0538: dt=0.028000, rms=0.517 (0.095%), neg=0, invalid=96777
- 0539: dt=0.028000, rms=0.517 (0.095%), neg=0, invalid=96777
- 0540: dt=0.028000, rms=0.516 (0.096%), neg=0, invalid=96777
- 0541: dt=0.028000, rms=0.516 (0.087%), neg=0, invalid=96777
- 0542: dt=0.028000, rms=0.515 (0.085%), neg=0, invalid=96777
- 0543: dt=0.028000, rms=0.515 (0.080%), neg=0, invalid=96777
- 0544: dt=0.028000, rms=0.514 (0.069%), neg=0, invalid=96777
- 0545: dt=0.028000, rms=0.514 (0.064%), neg=0, invalid=96777
- 0546: dt=0.028000, rms=0.514 (0.058%), neg=0, invalid=96777
- 0547: dt=0.028000, rms=0.514 (0.048%), neg=0, invalid=96777
- 0548: dt=0.028000, rms=0.513 (0.044%), neg=0, invalid=96777
- 0549: dt=0.028000, rms=0.513 (0.043%), neg=0, invalid=96777
- 0550: dt=0.028000, rms=0.513 (0.034%), neg=0, invalid=96777
- 0551: dt=0.028000, rms=0.513 (0.025%), neg=0, invalid=96777
- 0552: dt=0.028000, rms=0.513 (0.025%), neg=0, invalid=96777
- 0553: dt=0.028000, rms=0.513 (0.020%), neg=0, invalid=96777
- 0554: dt=0.000000, rms=0.513 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.513, neg=0, invalid=96777
- 0555: dt=0.448000, rms=0.507 (1.106%), neg=0, invalid=96777
- 0556: dt=0.000000, rms=0.507 (-0.000%), neg=0, invalid=96777
- 0557: dt=0.050000, rms=0.507 (-0.001%), 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=0.504, neg=0, invalid=96777
- 0558: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.504, neg=0, invalid=96777
- 0559: dt=129.472000, rms=0.504 (0.049%), neg=0, invalid=96777
- 0560: dt=129.472000, rms=0.504 (0.020%), neg=0, invalid=96777
- 0561: dt=129.472000, rms=0.504 (0.022%), neg=0, invalid=96777
- 0562: dt=129.472000, rms=0.504 (0.021%), neg=0, invalid=96777
- 0563: dt=129.472000, rms=0.504 (0.019%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.504, neg=0, invalid=96777
- 0564: dt=36.288000, rms=0.503 (0.149%), neg=0, invalid=96777
- 0565: dt=36.288000, rms=0.503 (0.071%), neg=0, invalid=96777
- 0566: dt=36.288000, rms=0.502 (0.060%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0567: dt=36.288000, rms=0.502 (0.049%), neg=0, invalid=96777
- 0568: dt=36.288000, rms=0.502 (-0.029%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.502, neg=0, invalid=96777
- 0569: dt=82.944000, rms=0.501 (0.325%), neg=0, invalid=96777
- 0570: dt=36.288000, rms=0.500 (0.156%), neg=0, invalid=96777
- 0571: dt=36.288000, rms=0.500 (0.017%), neg=0, invalid=96777
- 0572: dt=36.288000, rms=0.499 (0.116%), neg=0, invalid=96777
- 0573: dt=36.288000, rms=0.498 (0.149%), neg=0, invalid=96777
- 0574: dt=36.288000, rms=0.498 (0.130%), neg=0, invalid=96777
- 0575: dt=36.288000, rms=0.497 (0.109%), neg=0, invalid=96777
- 0576: dt=36.288000, rms=0.496 (0.134%), neg=0, invalid=96777
- 0577: dt=36.288000, rms=0.496 (0.099%), neg=0, invalid=96777
- 0578: dt=36.288000, rms=0.496 (0.087%), neg=0, invalid=96777
- 0579: dt=36.288000, rms=0.495 (0.024%), neg=0, invalid=96777
- 0580: dt=36.288000, rms=0.495 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.496, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0581: dt=38.400000, rms=0.493 (0.574%), neg=0, invalid=96777
- 0582: dt=11.200000, rms=0.492 (0.246%), neg=0, invalid=96777
- 0583: dt=11.200000, rms=0.491 (0.085%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0584: dt=11.200000, rms=0.490 (0.262%), neg=0, invalid=96777
- 0585: dt=11.200000, rms=0.489 (0.294%), neg=0, invalid=96777
- 0586: dt=11.200000, rms=0.487 (0.244%), neg=0, invalid=96777
- 0587: dt=11.200000, rms=0.487 (0.169%), neg=0, invalid=96777
- 0588: dt=11.200000, rms=0.485 (0.217%), neg=0, invalid=96777
- 0589: dt=11.200000, rms=0.485 (0.174%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0590: dt=11.200000, rms=0.484 (0.176%), neg=0, invalid=96777
- 0591: dt=11.200000, rms=0.483 (0.150%), neg=0, invalid=96777
- 0592: dt=11.200000, rms=0.482 (0.237%), neg=0, invalid=96777
- 0593: dt=11.200000, rms=0.481 (0.165%), neg=0, invalid=96777
- 0594: dt=11.200000, rms=0.480 (0.173%), neg=0, invalid=96777
- 0595: dt=11.200000, rms=0.480 (0.123%), neg=0, invalid=96777
- 0596: dt=11.200000, rms=0.479 (0.126%), neg=0, invalid=96777
- 0597: dt=11.200000, rms=0.479 (0.119%), neg=0, invalid=96777
- 0598: dt=11.200000, rms=0.478 (0.092%), neg=0, invalid=96777
- 0599: dt=11.200000, rms=0.478 (0.056%), neg=0, invalid=96777
- 0600: dt=11.200000, rms=0.478 (0.014%), neg=0, invalid=96777
- 0601: dt=11.200000, rms=0.478 (0.047%), neg=0, invalid=96777
- 0602: dt=11.200000, rms=0.477 (0.050%), neg=0, invalid=96777
- 0603: dt=11.200000, rms=0.477 (0.049%), neg=0, invalid=96777
- 0604: dt=11.200000, rms=0.477 (0.027%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.477, neg=0, invalid=96777
- 0605: dt=38.400000, rms=0.474 (0.529%), neg=0, invalid=96777
- 0606: dt=6.191571, rms=0.473 (0.204%), neg=0, invalid=96777
- 0607: dt=6.191571, rms=0.473 (0.083%), neg=0, invalid=96777
- 0608: dt=6.191571, rms=0.473 (0.090%), neg=0, invalid=96777
- 0609: dt=6.191571, rms=0.472 (0.099%), neg=0, invalid=96777
- 0610: dt=6.191571, rms=0.472 (0.112%), neg=0, invalid=96777
- 0611: dt=6.191571, rms=0.471 (0.101%), neg=0, invalid=96777
- 0612: dt=6.191571, rms=0.471 (0.075%), neg=0, invalid=96777
- 0613: dt=44.800000, rms=0.470 (0.098%), neg=0, invalid=96777
- 0614: dt=2.800000, rms=0.470 (0.006%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.476, neg=0, invalid=96777
- 0615: dt=4.148148, rms=0.476 (0.109%), neg=0, invalid=96777
- 0616: dt=2.880000, rms=0.476 (0.026%), neg=0, invalid=96777
- 0617: dt=2.880000, rms=0.475 (0.003%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 7 iterations, nbhd size=1, neg = 0
- 0618: dt=2.880000, rms=0.476 (-0.038%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.476, neg=0, invalid=96777
- iter 0, gcam->neg = 12
- after 11 iterations, nbhd size=1, neg = 0
- 0619: dt=8.597015, rms=0.475 (0.168%), neg=0, invalid=96777
- 0620: dt=1.008000, rms=0.475 (0.007%), neg=0, invalid=96777
- 0621: dt=1.008000, rms=0.475 (0.029%), neg=0, invalid=96777
- 0622: dt=1.008000, rms=0.474 (0.043%), neg=0, invalid=96777
- 0623: dt=1.008000, rms=0.474 (0.056%), neg=0, invalid=96777
- 0624: dt=1.008000, rms=0.474 (0.056%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0625: dt=1.008000, rms=0.474 (0.048%), neg=0, invalid=96777
- 0626: dt=1.008000, rms=0.473 (0.039%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.478, neg=0, invalid=96777
- 0627: dt=0.000000, rms=0.478 (0.001%), neg=0, invalid=96777
- 0628: dt=0.000000, rms=0.478 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.478, neg=0, invalid=96777
- 0629: dt=0.000000, rms=0.478 (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=0.470, neg=0, invalid=96777
- iter 0, gcam->neg = 801
- after 20 iterations, nbhd size=2, neg = 0
- 0630: dt=1.972211, rms=0.424 (9.755%), neg=0, invalid=96777
- 0631: dt=0.000078, rms=0.424 (-0.004%), neg=0, invalid=96777
- 0632: dt=0.000078, rms=0.424 (0.000%), neg=0, invalid=96777
- 0633: dt=0.000078, rms=0.424 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.424, neg=0, invalid=96777
- 0634: dt=0.000312, rms=0.424 (0.000%), neg=0, invalid=96777
- 0635: dt=0.000000, rms=0.424 (-0.002%), 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=0.405, neg=0, invalid=96777
- 0636: dt=0.000000, rms=0.407 (-0.323%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- 0637: dt=32.368000, rms=0.407 (0.004%), neg=0, invalid=96777
- 0638: dt=18.496000, rms=0.407 (0.000%), neg=0, invalid=96777
- 0639: dt=18.496000, rms=0.407 (-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=0.407, neg=0, invalid=96777
- 0640: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- 0641: dt=36.288000, rms=0.407 (0.020%), neg=0, invalid=96777
- 0642: dt=36.288000, rms=0.407 (0.007%), neg=0, invalid=96777
- 0643: dt=36.288000, rms=0.407 (0.006%), neg=0, invalid=96777
- 0644: dt=36.288000, rms=0.407 (0.006%), neg=0, invalid=96777
- 0645: dt=36.288000, rms=0.407 (0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.408, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0646: dt=11.200000, rms=0.407 (0.071%), neg=0, invalid=96777
- 0647: dt=8.000000, rms=0.407 (0.015%), neg=0, invalid=96777
- 0648: dt=8.000000, rms=0.407 (0.019%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0649: dt=8.000000, rms=0.407 (-0.011%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- iter 0, gcam->neg = 11
- after 8 iterations, nbhd size=1, neg = 0
- 0650: dt=44.800000, rms=0.405 (0.427%), neg=0, invalid=96777
- 0651: dt=11.200000, rms=0.405 (0.040%), neg=0, invalid=96777
- 0652: dt=11.200000, rms=0.405 (0.073%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 6 iterations, nbhd size=1, neg = 0
- 0653: dt=11.200000, rms=0.405 (0.108%), neg=0, invalid=96777
- 0654: dt=11.200000, rms=0.404 (0.010%), neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 200 iterations, nbhd size=4, neg = 1
- starting rms=0.004, neg=1, removing folds in lattice....
- iter 1, dt=0.000875: new neg 0, old_neg 1, delta 1, rms=0.003 (32.188%)
- 0655: dt=11.200000, rms=0.404 (-0.138%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.408, neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 7 iterations, nbhd size=1, neg = 0
- 0656: dt=2.880000, rms=0.407 (0.040%), neg=0, invalid=96777
- 0657: dt=0.201923, rms=0.407 (0.003%), neg=0, invalid=96777
- 0658: dt=0.201923, rms=0.407 (0.012%), neg=0, invalid=96777
- 0659: dt=0.201923, rms=0.407 (0.021%), neg=0, invalid=96777
- 0660: dt=0.201923, rms=0.407 (0.030%), neg=0, invalid=96777
- 0661: dt=0.201923, rms=0.407 (0.035%), neg=0, invalid=96777
- 0662: dt=0.201923, rms=0.407 (0.039%), neg=0, invalid=96777
- 0663: dt=0.201923, rms=0.407 (0.041%), neg=0, invalid=96777
- 0664: dt=0.201923, rms=0.406 (0.041%), neg=0, invalid=96777
- 0665: dt=0.201923, rms=0.406 (0.040%), 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 = 98
- after 23 iterations, nbhd size=2, neg = 0
- 0666: dt=13.824000, rms=0.404 (0.481%), neg=0, invalid=96777
- 0667: dt=0.003938, rms=0.404 (0.000%), neg=0, invalid=96777
- 0668: dt=0.003938, rms=0.404 (0.000%), neg=0, invalid=96777
- 0669: dt=0.003938, rms=0.404 (-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=0.411, neg=0, invalid=96777
- 0670: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.411, neg=0, invalid=96777
- 0671: dt=0.000000, rms=0.411 (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 = 627
- after 30 iterations, nbhd size=3, neg = 0
- 0672: dt=1.024000, rms=0.383 (4.222%), neg=0, invalid=96777
- 0673: dt=0.000000, rms=0.383 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 666
- after 9 iterations, nbhd size=1, neg = 0
- 0674: dt=0.050000, rms=0.383 (-0.435%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.383, neg=0, invalid=96777
- 0675: dt=0.000000, rms=0.383 (0.000%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 4 hours, 29 minutes and 33 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 16:34:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 16:36:11 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...
- 10536194 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 26 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 16:37:38 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=8.0
- skull bounding box = (44, 14, 11) --> (208, 205, 196)
- using (99, 78, 104) as brain centroid...
- mean wm in atlas = 126, using box (79,54,81) --> (119, 101,126) 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
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.012 -0.016 -0.073 6.601;
- 0.037 1.037 0.374 -26.429;
- 0.067 -0.358 0.912 30.424;
- 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=-3.9)
- 1.012 -0.016 -0.073 6.601;
- 0.037 1.037 0.374 -26.429;
- 0.067 -0.358 0.912 30.424;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-3.9)
- 1.009 -0.016 -0.072 7.020;
- 0.036 1.034 0.373 -25.911;
- 0.068 -0.358 0.914 30.247;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.010 -0.016 -0.072 6.881;
- 0.036 1.033 0.372 -25.739;
- 0.068 -0.359 0.915 30.158;
- 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
- 1.00975 -0.01640 -0.07248 6.88051;
- 0.03639 1.03251 0.37245 -25.73854;
- 0.06766 -0.35886 0.91506 30.15802;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.00975 -0.01640 -0.07248 6.88051;
- 0.03639 1.03251 0.37245 -25.73854;
- 0.06766 -0.35886 0.91506 30.15802;
- 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:
- 1.010 -0.016 -0.072 6.881;
- 0.036 1.033 0.372 -25.739;
- 0.068 -0.359 0.915 30.158;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.1)
- transform before final EM align:
- 1.010 -0.016 -0.072 6.881;
- 0.036 1.033 0.372 -25.739;
- 0.068 -0.359 0.915 30.158;
- 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
- 1.00975 -0.01640 -0.07248 6.88051;
- 0.03639 1.03251 0.37245 -25.73854;
- 0.06766 -0.35886 0.91506 30.15802;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.00975 -0.01640 -0.07248 6.88051;
- 0.03639 1.03251 0.37245 -25.73854;
- 0.06766 -0.35886 0.91506 30.15802;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 008: -log(p) = 4.4
- after pass:transform: ( 1.01, -0.02, -0.07, 6.88)
- ( 0.04, 1.03, 0.37, -25.74)
- ( 0.07, -0.36, 0.92, 30.16)
- dfp_em_step_func: 009: -log(p) = 4.4
- after pass:transform: ( 1.01, -0.02, -0.07, 6.88)
- ( 0.04, 1.03, 0.37, -25.74)
- ( 0.07, -0.36, 0.92, 30.16)
- dfp_em_step_func: 010: -log(p) = 4.4
- after pass:transform: ( 1.01, -0.02, -0.07, 6.88)
- ( 0.04, 1.03, 0.37, -25.74)
- ( 0.07, -0.36, 0.92, 30.16)
- 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 TOLERANCESpass 2 through quasi-newton minimization...
- dfp_em_step_func: 011: -log(p) = 4.4
- after pass:transform: ( 1.01, -0.02, -0.07, 6.88)
- ( 0.04, 1.03, 0.37, -25.74)
- ( 0.07, -0.36, 0.92, 30.16)
- 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 TOLERANCESpass 3 through quasi-newton minimization...
- 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: 013: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.011 -0.016 -0.072 6.881;
- 0.037 1.033 0.373 -25.739;
- 0.068 -0.358 0.915 30.158;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 40 minutes and 13 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 17:17:50 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/sub002/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 = 0.11505 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (4274 voxels, overlap=0.007)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (4274 voxels, peak = 7), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.12347 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.35 x + 0.0 (851 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (851 voxels, peak = 7), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.09091 (91)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (335 voxels, overlap=0.241)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (335 voxels, peak = 89), gca=88.8
- gca peak = 0.18160 (96)
- mri peak = 0.11747 (92)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (338 voxels, overlap=0.404)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (338 voxels, peak = 88), gca=87.8
- gca peak = 0.27536 (62)
- mri peak = 0.07051 (58)
- Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (593 voxels, overlap=0.776)
- Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (593 voxels, peak = 57), gca=56.7
- gca peak = 0.32745 (63)
- mri peak = 0.07543 (62)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (637 voxels, overlap=0.996)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (637 voxels, peak = 58), gca=58.3
- gca peak = 0.08597 (105)
- mri peak = 0.08677 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45112 voxels, overlap=0.700)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45112 voxels, peak = 107), gca=106.6
- gca peak = 0.09209 (106)
- mri peak = 0.08778 (109)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (45509 voxels, overlap=0.613)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (45509 voxels, peak = 109), gca=108.6
- gca peak = 0.07826 (63)
- mri peak = 0.04953 (54)
- Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (17016 voxels, overlap=0.594)
- Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (17016 voxels, peak = 55), gca=55.1
- gca peak = 0.08598 (64)
- mri peak = 0.04978 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (16497 voxels, overlap=0.424)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (16497 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.09000 (70)
- Right_Caudate (50): linear fit = 0.94 x + 0.0 (700 voxels, overlap=1.013)
- Right_Caudate (50): linear fit = 0.94 x + 0.0 (700 voxels, peak = 67), gca=67.1
- gca peak = 0.18227 (75)
- mri peak = 0.09213 (68)
- Left_Caudate (11): linear fit = 0.89 x + 0.0 (966 voxels, overlap=0.499)
- Left_Caudate (11): linear fit = 0.89 x + 0.0 (966 voxels, peak = 67), gca=67.1
- gca peak = 0.10629 (62)
- mri peak = 0.04739 (51)
- Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (10282 voxels, overlap=0.861)
- Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (10282 voxels, peak = 57), gca=56.7
- gca peak = 0.11668 (59)
- mri peak = 0.05057 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10639 voxels, overlap=0.913)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10639 voxels, peak = 54), gca=54.0
- gca peak = 0.17849 (88)
- mri peak = 0.08393 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5434 voxels, overlap=0.960)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5434 voxels, peak = 90), gca=90.2
- gca peak = 0.16819 (86)
- mri peak = 0.08571 (90)
- Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4938 voxels, overlap=0.973)
- Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4938 voxels, peak = 88), gca=88.2
- gca peak = 0.41688 (64)
- mri peak = 0.10288 (63)
- Left_Amygdala (18): linear fit = 1.05 x + 0.0 (241 voxels, overlap=1.023)
- Left_Amygdala (18): linear fit = 1.05 x + 0.0 (241 voxels, peak = 68), gca=67.5
- gca peak = 0.42394 (62)
- mri peak = 0.07365 (58)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (353 voxels, overlap=1.041)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (353 voxels, peak = 58), gca=58.0
- gca peak = 0.10041 (96)
- mri peak = 0.06711 (91)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3327 voxels, overlap=0.967)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3327 voxels, peak = 93), gca=92.6
- gca peak = 0.13978 (88)
- mri peak = 0.06244 (88)
- Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3162 voxels, overlap=0.952)
- Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3162 voxels, peak = 86), gca=85.8
- gca peak = 0.08514 (81)
- mri peak = 0.06388 (79)
- Left_Putamen (12): linear fit = 0.94 x + 0.0 (2191 voxels, overlap=0.679)
- Left_Putamen (12): linear fit = 0.94 x + 0.0 (2191 voxels, peak = 76), gca=75.7
- gca peak = 0.09624 (82)
- mri peak = 0.06533 (71)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1548 voxels, overlap=0.574)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1548 voxels, peak = 73), gca=72.6
- gca peak = 0.07543 (88)
- mri peak = 0.06900 (90)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10325 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10325 voxels, peak = 91), gca=91.1
- gca peak = 0.12757 (95)
- mri peak = 0.06142 (97)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (973 voxels, overlap=0.820)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (973 voxels, peak = 99), gca=99.3
- gca peak = 0.17004 (92)
- mri peak = 0.06630 (100)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1154 voxels, overlap=0.859)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1154 voxels, peak = 95), gca=95.2
- gca peak = 0.21361 (36)
- mri peak = 0.20312 (13)
- Third_Ventricle (14): linear fit = 0.34 x + 0.0 (64 voxels, overlap=0.060)
- Third_Ventricle (14): linear fit = 0.34 x + 0.0 (64 voxels, peak = 12), gca=12.1
- gca peak = 0.26069 (23)
- mri peak = 0.12873 (13)
- Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (315 voxels, overlap=0.027)
- Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (315 voxels, peak = 9), gca=8.9
- 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 0.92 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 = 0.11505 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (4274 voxels, overlap=0.942)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (4274 voxels, peak = 8), gca=7.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.12347 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (851 voxels, overlap=0.997)
- Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (851 voxels, peak = 8), gca=8.3
- gca peak = 0.32313 (89)
- mri peak = 0.09091 (91)
- Right_Pallidum (52): linear fit = 0.98 x + 0.0 (335 voxels, overlap=1.012)
- Right_Pallidum (52): linear fit = 0.98 x + 0.0 (335 voxels, peak = 87), gca=86.8
- gca peak = 0.19545 (88)
- mri peak = 0.11747 (92)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (338 voxels, overlap=1.003)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (338 voxels, peak = 88), gca=88.0
- gca peak = 0.30131 (57)
- mri peak = 0.07051 (58)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (593 voxels, overlap=1.007)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (593 voxels, peak = 57), gca=57.0
- gca peak = 0.28488 (58)
- mri peak = 0.07543 (62)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (637 voxels, overlap=1.008)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (637 voxels, peak = 58), gca=58.0
- gca peak = 0.08542 (107)
- mri peak = 0.08677 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45112 voxels, overlap=0.742)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45112 voxels, peak = 107), gca=107.0
- gca peak = 0.08551 (108)
- mri peak = 0.08778 (109)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45509 voxels, overlap=0.708)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45509 voxels, peak = 109), gca=108.5
- gca peak = 0.08996 (55)
- mri peak = 0.04953 (54)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17016 voxels, overlap=0.975)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17016 voxels, peak = 54), gca=54.2
- gca peak = 0.10529 (53)
- mri peak = 0.04978 (51)
- Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16497 voxels, overlap=0.975)
- Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16497 voxels, peak = 53), gca=53.0
- gca peak = 0.22918 (67)
- mri peak = 0.09000 (70)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (700 voxels, overlap=1.007)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (700 voxels, peak = 67), gca=67.0
- gca peak = 0.18268 (67)
- mri peak = 0.09213 (68)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (966 voxels, overlap=0.999)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (966 voxels, peak = 67), gca=67.0
- gca peak = 0.11904 (56)
- mri peak = 0.04739 (51)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10282 voxels, overlap=1.000)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10282 voxels, peak = 55), gca=55.2
- gca peak = 0.13094 (55)
- mri peak = 0.05057 (56)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10639 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10639 voxels, peak = 56), gca=56.4
- gca peak = 0.16673 (89)
- mri peak = 0.08393 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5434 voxels, overlap=0.990)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5434 voxels, peak = 89), gca=88.6
- gca peak = 0.14595 (89)
- mri peak = 0.08571 (90)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4938 voxels, overlap=0.996)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4938 voxels, peak = 89), gca=88.6
- gca peak = 0.33140 (67)
- mri peak = 0.10288 (63)
- Left_Amygdala (18): linear fit = 0.95 x + 0.0 (241 voxels, overlap=0.955)
- Left_Amygdala (18): linear fit = 0.95 x + 0.0 (241 voxels, peak = 64), gca=64.0
- gca peak = 0.48017 (58)
- mri peak = 0.07365 (58)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (353 voxels, overlap=1.027)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (353 voxels, peak = 58), gca=58.0
- gca peak = 0.10197 (93)
- mri peak = 0.06711 (91)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3327 voxels, overlap=0.983)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3327 voxels, peak = 94), gca=94.4
- gca peak = 0.11274 (83)
- mri peak = 0.06244 (88)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3162 voxels, overlap=0.998)
- Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3162 voxels, peak = 84), gca=84.2
- gca peak = 0.09445 (77)
- mri peak = 0.06388 (79)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (2191 voxels, overlap=0.991)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (2191 voxels, peak = 76), gca=75.8
- gca peak = 0.12421 (67)
- mri peak = 0.06533 (71)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1548 voxels, overlap=1.001)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1548 voxels, peak = 67), gca=67.0
- gca peak = 0.07025 (88)
- mri peak = 0.06900 (90)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (10325 voxels, overlap=0.836)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (10325 voxels, peak = 88), gca=87.6
- gca peak = 0.13021 (99)
- mri peak = 0.06142 (97)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (973 voxels, overlap=0.871)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (973 voxels, peak = 99), gca=99.5
- gca peak = 0.13821 (95)
- mri peak = 0.06630 (100)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1154 voxels, overlap=0.917)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1154 voxels, peak = 95), gca=95.0
- gca peak = 0.35640 (14)
- mri peak = 0.20312 (13)
- Third_Ventricle (14): linear fit = 0.82 x + 0.0 (64 voxels, overlap=0.739)
- Third_Ventricle (14): linear fit = 0.82 x + 0.0 (64 voxels, peak = 12), gca=11.6
- gca peak = 0.33827 ( 9)
- mri peak = 0.12873 (13)
- Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (315 voxels, overlap=0.963)
- Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (315 voxels, peak = 9), gca=9.5
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.24950 (33)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.42363 (63)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.59104 (62)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.34941 (29)
- gca peak Right_Accumbens_area = 0.31038 (68)
- gca peak Right_vessel = 0.58297 (60)
- gca peak Right_choroid_plexus = 0.10278 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17311 (83)
- gca peak non_WM_hypointensities = 0.12130 (54)
- gca peak Optic_Chiasm = 0.34840 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.99 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.88 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
- 15871 gm and wm labels changed (%11 to gray, %89 to white out of all changed labels)
- 395 hippocampal voxels changed.
- 6 amygdala voxels changed.
- pass 1: 107856 changed. image ll: -2.278, PF=1.000
- pass 2: 19554 changed. image ll: -2.276, PF=1.000
- pass 3: 7651 changed.
- pass 4: 3459 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 19 minutes and 50 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/cc_up.lta sub002
- 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/sub002/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/norm.mgz
- 39080 voxels in left wm, 38159 in right wm, xrange [122, 132]
- searching rotation angles z=[-6 8], y=[-9 5]
-
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
searching scale 1 Z rot 6.2
searching scale 1 Z rot 6.4
searching scale 1 Z rot 6.7
searching scale 1 Z rot 6.9
searching scale 1 Z rot 7.2 global minimum found at slice 126.0, rotations (-2.05, 0.43)
- final transformation (x=126.0, yr=-2.053, zr=0.432):
- 0.999 -0.008 -0.036 6.142;
- 0.008 1.000 -0.000 45.078;
- 0.036 -0.000 0.999 27.549;
- 0.000 0.000 0.000 1.000;
- updating x range to be [125, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 149 126
- eigenvectors:
- -0.002 0.004 1.000;
- -0.215 -0.977 0.003;
- 0.977 -0.215 0.003;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 0.9 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 17:38:36 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 17:38:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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...
- 4572 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 56 (56), valley at 31 (31)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at -nan
- white matter peak found at 0
- gm peak at 0 (0), valley at 6 (-10)
- csf peak at 0, setting threshold to 0
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 21 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 17:42:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1872837 voxels in mask (pct= 11.16)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 17:43:01 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (107.0): 107.0 +- 4.6 [80.0 --> 125.0]
- GM (68.0) : 67.1 +- 9.4 [30.0 --> 96.0]
- setting bottom of white matter range to 76.5
- setting top of gray matter range to 85.9
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- using local geometry to label remaining ambiguous voxels...
- reclassifying voxels using Gaussian border classifier...
- removing voxels with positive offset direction...
- smoothing T1 volume with sigma = 0.250
- removing 1-dimensional structures...
- 7323 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 6642 filled
- 286 bright non-wm voxels segmented.
- 3956 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 0.64 minutes
- reading wm segmentation from wm.seg.mgz...
- 170 voxels added to wm to prevent paths from MTL structures to cortex
- 1820 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 66007 voxels turned on, 38907 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+): 23 found - 23 modified | TOTAL: 23
- pass 2 (xy+): 0 found - 23 modified | TOTAL: 23
- pass 1 (xy-): 19 found - 19 modified | TOTAL: 42
- pass 2 (xy-): 0 found - 19 modified | TOTAL: 42
- pass 1 (yz+): 45 found - 45 modified | TOTAL: 87
- pass 2 (yz+): 0 found - 45 modified | TOTAL: 87
- pass 1 (yz-): 19 found - 19 modified | TOTAL: 106
- pass 2 (yz-): 0 found - 19 modified | TOTAL: 106
- pass 1 (xz+): 23 found - 23 modified | TOTAL: 129
- pass 2 (xz+): 0 found - 23 modified | TOTAL: 129
- pass 1 (xz-): 26 found - 26 modified | TOTAL: 155
- pass 2 (xz-): 0 found - 26 modified | TOTAL: 155
- Iteration Number : 1
- pass 1 (+++): 13 found - 13 modified | TOTAL: 13
- pass 2 (+++): 0 found - 13 modified | TOTAL: 13
- pass 1 (+++): 14 found - 14 modified | TOTAL: 27
- pass 2 (+++): 0 found - 14 modified | TOTAL: 27
- pass 1 (+++): 9 found - 9 modified | TOTAL: 36
- pass 2 (+++): 0 found - 9 modified | TOTAL: 36
- pass 1 (+++): 15 found - 15 modified | TOTAL: 51
- pass 2 (+++): 0 found - 15 modified | TOTAL: 51
- Iteration Number : 1
- pass 1 (++): 171 found - 171 modified | TOTAL: 171
- pass 2 (++): 0 found - 171 modified | TOTAL: 171
- pass 1 (+-): 162 found - 162 modified | TOTAL: 333
- pass 2 (+-): 0 found - 162 modified | TOTAL: 333
- pass 1 (--): 149 found - 149 modified | TOTAL: 482
- pass 2 (--): 0 found - 149 modified | TOTAL: 482
- pass 1 (-+): 144 found - 144 modified | TOTAL: 626
- pass 2 (-+): 0 found - 144 modified | TOTAL: 626
- Iteration Number : 2
- pass 1 (xy+): 9 found - 9 modified | TOTAL: 9
- pass 2 (xy+): 0 found - 9 modified | TOTAL: 9
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 10
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 10
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 12
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 12
- pass 1 (yz-): 7 found - 7 modified | TOTAL: 19
- pass 2 (yz-): 0 found - 7 modified | TOTAL: 19
- pass 1 (xz+): 5 found - 5 modified | TOTAL: 24
- pass 2 (xz+): 0 found - 5 modified | TOTAL: 24
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 27
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 27
- 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 (+-): 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
- pass 1 (-+): 3 found - 3 modified | TOTAL: 6
- pass 2 (-+): 0 found - 3 modified | TOTAL: 6
- 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-): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 1
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
- 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
- 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-): 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 : 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
- Total Number of Modified Voxels = 866 (out of 661130: 0.130988)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 17:45:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.035 0.007 -0.030 -3.248;
- 0.002 1.039 0.311 -15.351;
- 0.034 -0.278 0.903 29.756;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1245 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75)
- no need to search
- using seed (126, 117, 152), TAL = (2.0, 24.0, 11.0)
- talairach voxel to voxel transform
- 0.965 0.002 0.031 2.228;
- 0.008 0.881 -0.304 22.582;
- -0.034 0.271 1.013 -26.103;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (126, 117, 152) --> (2.0, 24.0, 11.0)
- done.
- writing output to filled.mgz...
- filling took 1.0 minutes
- talairach cc position changed to (2.00, 24.00, 11.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, 24.00, 11.00) SRC: (111.51, 80.37, 155.99)
- search lh wm seed point around talairach space (-16.00, 24.00, 11.00), SRC: (146.26, 80.66, 154.78)
- 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 17:46:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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-): 1 found - 1 modified | TOTAL: 3
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 3
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 5
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 5
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 6
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 6
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 7
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 7
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 8
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 8
- 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 (+-): 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 (-+): 1 found - 1 modified | TOTAL: 3
- pass 2 (-+): 0 found - 1 modified | TOTAL: 3
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy-): 0 found - 1 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 = 12 (out of 324847: 0.003694)
- 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: 485 vertices, 568 faces
- slice 40: 6210 vertices, 6507 faces
- slice 50: 17096 vertices, 17505 faces
- slice 60: 29888 vertices, 30345 faces
- slice 70: 42910 vertices, 43345 faces
- slice 80: 55489 vertices, 55876 faces
- slice 90: 67710 vertices, 68128 faces
- slice 100: 79985 vertices, 80380 faces
- slice 110: 92245 vertices, 92655 faces
- slice 120: 103998 vertices, 104425 faces
- slice 130: 115128 vertices, 115553 faces
- slice 140: 125639 vertices, 126012 faces
- slice 150: 134522 vertices, 134849 faces
- slice 160: 142620 vertices, 142891 faces
- slice 170: 149792 vertices, 150016 faces
- slice 180: 156163 vertices, 156379 faces
- slice 190: 161191 vertices, 161357 faces
- slice 200: 163288 vertices, 163328 faces
- slice 210: 163318 vertices, 163342 faces
- slice 220: 163318 vertices, 163342 faces
- slice 230: 163318 vertices, 163342 faces
- slice 240: 163318 vertices, 163342 faces
- slice 250: 163318 vertices, 163342 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...
- 163318 voxel in cpt #1: X=-24 [v=163318,e=490026,f=326684] located at (-27.214685, -24.672211, 39.221371)
- For the whole surface: X=-24 [v=163318,e=490026,f=326684]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 17:46:46 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 17:46:51 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- avg radius = 51.3 mm, total surface area = 86638 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.098 (target=0.015)
step 005: RMS=0.073 (target=0.015)
step 010: RMS=0.055 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.035 (target=0.015)
step 030: RMS=0.032 (target=0.015)
step 035: RMS=0.030 (target=0.015)
step 040: RMS=0.027 (target=0.015)
step 045: RMS=0.027 (target=0.015)
step 050: RMS=0.026 (target=0.015)
step 055: RMS=0.026 (target=0.015)
step 060: RMS=0.025 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 17:47:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 0.90 +- 0.55 (0.00-->5.85) (max @ vno 121281 --> 121282)
- face area 0.02 +- 0.03 (-0.17-->0.59)
- scaling brain by 0.288...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.145, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.884, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.323, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.585, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.745, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.847, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.920, avgs=0
- 035/300: dt: 0.9000, rms radial error=170.977, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.026, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.073, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.123, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.180, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.241, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.306, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.376, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.450, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.529, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.613, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.703, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.798, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.898, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.004, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.114, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.229, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.350, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.475, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.605, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.740, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.881, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.026, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.176, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.330, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.490, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.654, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.823, avgs=0
- 175/300: dt: 0.9000, rms radial error=145.997, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.175, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.358, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.546, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.739, avgs=0
- 200/300: dt: 0.9000, rms radial error=141.935, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.137, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.342, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.552, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.767, avgs=0
- 225/300: dt: 0.9000, rms radial error=137.986, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.209, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.436, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.668, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.904, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.145, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.390, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.639, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.892, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.149, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.411, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.677, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.947, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.221, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.498, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.780, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 19550.91
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
- epoch 2 (K=40.0), pass 1, starting sse = 3446.64
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00005
- epoch 3 (K=160.0), pass 1, starting sse = 388.06
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.06/11 = 0.00507
- epoch 4 (K=640.0), pass 1, starting sse = 24.11
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.09/12 = 0.00732
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.09 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 17:53:01 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/sub002/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub002 lh
- reading spherical homeomorphism from 'qsphere.nofix'
- using genetic algorithm with optimized parameters
- setting seed for random number genererator to 1234
- *************************************************************
- Topology Correction Parameters
- retessellation mode: genetic search
- number of patches/generation : 10
- number of generations : 10
- surface mri loglikelihood coefficient : 1.0
- volume mri loglikelihood coefficient : 10.0
- normal dot loglikelihood coefficient : 1.0
- quadratic curvature loglikelihood coefficient : 1.0
- volume resolution : 2
- eliminate vertices during search : 1
- initial patch selection : 1
- select all defect vertices : 0
- ordering dependant retessellation: 0
- use precomputed edge table : 0
- smooth retessellated patch : 2
- match retessellated patch : 1
- verbose mode : 0
- *************************************************************
- INFO: assuming .mgz format
- $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- before topology correction, eno=-24 (nv=163318, nf=326684, ne=490026, g=13)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 10 iterations
- marking ambiguous vertices...
- 2474 ambiguous faces found in tessellation
- segmenting defects...
- 29 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 29 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7221 (-4.8611)
- -vertex loglikelihood: -6.5993 (-3.2997)
- -normal dot loglikelihood: -3.6464 (-3.6464)
- -quad curv loglikelihood: -6.3981 (-3.1990)
- Total Loglikelihood : -26.3659
- CORRECTING DEFECT 0 (vertices=5, convex hull=21)
- After retessellation of defect 0, euler #=-25 (161818,484953,323110) : difference with theory (-26) = -1
- CORRECTING DEFECT 1 (vertices=83, convex hull=56)
- After retessellation of defect 1, euler #=-24 (161828,485006,323154) : difference with theory (-25) = -1
- CORRECTING DEFECT 2 (vertices=51, convex hull=50)
- After retessellation of defect 2, euler #=-23 (161840,485058,323195) : difference with theory (-24) = -1
- CORRECTING DEFECT 3 (vertices=74, convex hull=72)
- After retessellation of defect 3, euler #=-22 (161856,485133,323255) : difference with theory (-23) = -1
- CORRECTING DEFECT 4 (vertices=9, convex hull=32)
- After retessellation of defect 4, euler #=-21 (161857,485143,323265) : difference with theory (-22) = -1
- CORRECTING DEFECT 5 (vertices=9, convex hull=26)
- After retessellation of defect 5, euler #=-20 (161859,485156,323277) : difference with theory (-21) = -1
- CORRECTING DEFECT 6 (vertices=26, convex hull=31)
- After retessellation of defect 6, euler #=-19 (161863,485176,323294) : difference with theory (-20) = -1
- CORRECTING DEFECT 7 (vertices=25, convex hull=48)
- After retessellation of defect 7, euler #=-18 (161872,485221,323331) : difference with theory (-19) = -1
- CORRECTING DEFECT 8 (vertices=5, convex hull=18)
- After retessellation of defect 8, euler #=-17 (161872,485225,323336) : difference with theory (-18) = -1
- CORRECTING DEFECT 9 (vertices=304, convex hull=132)
- After retessellation of defect 9, euler #=-17 (161975,485611,323619) : difference with theory (-17) = 0
- CORRECTING DEFECT 10 (vertices=129, convex hull=48)
- After retessellation of defect 10, euler #=-16 (161987,485669,323666) : difference with theory (-16) = 0
- CORRECTING DEFECT 11 (vertices=42, convex hull=26)
- After retessellation of defect 11, euler #=-15 (161991,485688,323682) : difference with theory (-15) = 0
- CORRECTING DEFECT 12 (vertices=156, convex hull=66)
- After retessellation of defect 12, euler #=-14 (162016,485786,323756) : difference with theory (-14) = 0
- CORRECTING DEFECT 13 (vertices=15, convex hull=13)
- After retessellation of defect 13, euler #=-13 (162017,485795,323765) : difference with theory (-13) = 0
- CORRECTING DEFECT 14 (vertices=13, convex hull=27)
- After retessellation of defect 14, euler #=-12 (162022,485819,323785) : difference with theory (-12) = 0
- CORRECTING DEFECT 15 (vertices=46, convex hull=24)
- After retessellation of defect 15, euler #=-11 (162027,485840,323802) : difference with theory (-11) = 0
- CORRECTING DEFECT 16 (vertices=33, convex hull=59)
- After retessellation of defect 16, euler #=-10 (162051,485934,323873) : difference with theory (-10) = 0
- CORRECTING DEFECT 17 (vertices=35, convex hull=62)
- After retessellation of defect 17, euler #=-9 (162069,486013,323935) : difference with theory (-9) = 0
- CORRECTING DEFECT 18 (vertices=38, convex hull=29)
- After retessellation of defect 18, euler #=-8 (162073,486034,323953) : difference with theory (-8) = 0
- CORRECTING DEFECT 19 (vertices=24, convex hull=62)
- After retessellation of defect 19, euler #=-7 (162083,486084,323994) : difference with theory (-7) = 0
- CORRECTING DEFECT 20 (vertices=21, convex hull=48)
- After retessellation of defect 20, euler #=-6 (162093,486131,324032) : difference with theory (-6) = 0
- CORRECTING DEFECT 21 (vertices=33, convex hull=32)
- After retessellation of defect 21, euler #=-5 (162100,486163,324058) : difference with theory (-5) = 0
- CORRECTING DEFECT 22 (vertices=104, convex hull=108)
- After retessellation of defect 22, euler #=-4 (162142,486334,324188) : difference with theory (-4) = 0
- CORRECTING DEFECT 23 (vertices=28, convex hull=43)
- After retessellation of defect 23, euler #=-3 (162151,486374,324220) : difference with theory (-3) = 0
- CORRECTING DEFECT 24 (vertices=35, convex hull=21)
- After retessellation of defect 24, euler #=-2 (162154,486389,324233) : difference with theory (-2) = 0
- CORRECTING DEFECT 25 (vertices=34, convex hull=33)
- After retessellation of defect 25, euler #=-1 (162156,486404,324247) : difference with theory (-1) = 0
- CORRECTING DEFECT 26 (vertices=35, convex hull=34)
- After retessellation of defect 26, euler #=0 (162160,486427,324267) : difference with theory (0) = 0
- CORRECTING DEFECT 27 (vertices=51, convex hull=54)
- After retessellation of defect 27, euler #=1 (162164,486458,324295) : difference with theory (1) = 0
- CORRECTING DEFECT 28 (vertices=37, convex hull=69)
- After retessellation of defect 28, euler #=2 (162178,486528,324352) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.08-->7.26) (max @ vno 125026 --> 130478)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.21 (0.08-->7.26) (max @ vno 125026 --> 130478)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 92 mutations (36.5%), 160 crossovers (63.5%), 16 vertices were eliminated
- building final representation...
- 1140 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=162178, nf=324352, ne=486528, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 15.4 minutes
- 0 defective edges
- removing intersecting faces
- 000: 143 intersecting
- 001: 17 intersecting
- 002: 7 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 162178 - 486528 + 324352 = 2 --> 0 holes
- F =2V-4: 324352 = 324356-4 (0)
- 2E=3F: 973056 = 973056 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 53 intersecting
- 001: 11 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 18:08:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub002 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/sub002/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- 20389 bright wm thresholded.
- 326 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.orig...
- computing class statistics...
- border white: 305608 voxels (1.82%)
- border gray 333888 voxels (1.99%)
- WM (92.0): 93.4 +- 9.7 [70.0 --> 110.0]
- GM (76.0) : 74.6 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 48.3 (was 70)
- setting MAX_BORDER_WHITE to 114.7 (was 105)
- setting MIN_BORDER_WHITE to 61.0 (was 85)
- setting MAX_CSF to 35.6 (was 40)
- setting MAX_GRAY to 95.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 54.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 22.8 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.02-->2.48) (max @ vno 117773 --> 118787)
- face area 0.28 +- 0.12 (0.00-->2.11)
- mean absolute distance = 0.77 +- 0.96
- 3703 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=61
- mean inside = 92.7, mean outside = 69.6
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=73.1, 146 (146) missing vertices, mean dist 0.3 [0.7 (%29.1)->0.8 (%70.9))]
- %61 local maxima, %34 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 (0.10-->3.38) (max @ vno 112452 --> 112451)
- face area 0.28 +- 0.13 (0.00-->1.76)
- mean absolute distance = 0.38 +- 0.56
- 3448 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8275687.5, rms=13.32
- 001: dt: 0.5000, sse=8102511.5, rms=9.539 (0.000%)
- 002: dt: 0.5000, sse=8188070.0, rms=7.205 (0.000%)
- 003: dt: 0.5000, sse=8436538.0, rms=5.718 (0.000%)
- 004: dt: 0.5000, sse=8620744.0, rms=4.844 (0.000%)
- 005: dt: 0.5000, sse=8857631.0, rms=4.370 (0.000%)
- 006: dt: 0.5000, sse=8930440.0, rms=4.154 (0.000%)
- 007: dt: 0.5000, sse=9014043.0, rms=4.034 (0.000%)
- 008: dt: 0.5000, sse=9003889.0, rms=3.978 (0.000%)
- rms = 3.93, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=8987069.0, rms=3.929 (0.000%)
- 010: dt: 0.2500, sse=5421268.5, rms=2.665 (0.000%)
- 011: dt: 0.2500, sse=4922603.5, rms=2.224 (0.000%)
- 012: dt: 0.2500, sse=4626893.0, rms=2.112 (0.000%)
- 013: dt: 0.2500, sse=4541714.5, rms=2.024 (0.000%)
- rms = 1.99, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4449954.5, rms=1.994 (0.000%)
- 015: dt: 0.1250, sse=4288910.0, rms=1.854 (0.000%)
- rms = 1.84, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4247179.5, rms=1.838 (0.000%)
- positioning took 2.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=78.3, 112 (47) missing vertices, mean dist -0.3 [0.4 (%79.8)->0.2 (%20.2))]
- %77 local maxima, %18 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-->3.74) (max @ vno 106914 --> 105889)
- face area 0.35 +- 0.16 (0.00-->2.19)
- mean absolute distance = 0.23 +- 0.32
- 3000 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5696138.0, rms=6.74
- 017: dt: 0.5000, sse=5571937.5, rms=4.228 (0.000%)
- rms = 4.24, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5077418.0, rms=3.235 (0.000%)
- 019: dt: 0.2500, sse=4817492.0, rms=2.390 (0.000%)
- 020: dt: 0.2500, sse=4722547.0, rms=1.904 (0.000%)
- 021: dt: 0.2500, sse=4667988.5, rms=1.772 (0.000%)
- 022: dt: 0.2500, sse=4593165.0, rms=1.665 (0.000%)
- rms = 1.63, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4583835.0, rms=1.630 (0.000%)
- 024: dt: 0.1250, sse=4465102.0, rms=1.507 (0.000%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4428838.5, rms=1.498 (0.000%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- mean border=81.8, 91 (22) missing vertices, mean dist -0.2 [0.2 (%77.5)->0.2 (%22.5))]
- %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.07-->4.01) (max @ vno 106914 --> 105889)
- face area 0.34 +- 0.16 (0.00-->2.55)
- mean absolute distance = 0.17 +- 0.25
- 2769 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4949801.0, rms=4.50
- 026: dt: 0.5000, sse=5238463.5, rms=3.727 (0.000%)
- rms = 3.99, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4745555.0, rms=2.357 (0.000%)
- 028: dt: 0.2500, sse=4624449.0, rms=1.850 (0.000%)
- 029: dt: 0.2500, sse=4652733.0, rms=1.542 (0.000%)
- rms = 1.56, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4593124.0, rms=1.451 (0.000%)
- 031: dt: 0.1250, sse=4516467.0, rms=1.325 (0.000%)
- rms = 1.32, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4479426.5, rms=1.317 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=82.8, 99 (18) missing vertices, mean dist -0.0 [0.2 (%58.1)->0.2 (%41.9))]
- %91 local maxima, % 5 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/sub002/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=4515783.0, rms=1.79
- rms = 2.50, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4611573.5, rms=1.170 (0.000%)
- 034: dt: 0.2500, sse=4788554.5, rms=0.994 (0.000%)
- rms = 1.00, time step reduction 2 of 3 to 0.125...
- rms = 0.99, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4788534.5, rms=0.986 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 17 non-cortical segments detected
- only using segment with 1848 vertices
- erasing segment 1 (vno[0] = 79279)
- erasing segment 2 (vno[0] = 97128)
- erasing segment 3 (vno[0] = 101552)
- erasing segment 4 (vno[0] = 106865)
- erasing segment 5 (vno[0] = 108150)
- erasing segment 6 (vno[0] = 115908)
- erasing segment 7 (vno[0] = 118885)
- erasing segment 8 (vno[0] = 121878)
- erasing segment 9 (vno[0] = 122931)
- erasing segment 10 (vno[0] = 122941)
- erasing segment 11 (vno[0] = 122951)
- erasing segment 12 (vno[0] = 123936)
- erasing segment 13 (vno[0] = 125845)
- erasing segment 14 (vno[0] = 129542)
- erasing segment 15 (vno[0] = 129579)
- erasing segment 16 (vno[0] = 130372)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.area
- vertex spacing 0.89 +- 0.25 (0.06-->4.08) (max @ vno 106914 --> 105889)
- face area 0.33 +- 0.16 (0.00-->2.68)
- refinement took 8.1 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 18:16:43 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 18:16:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 51.5 mm, total surface area = 98637 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.112 (target=0.015)
step 005: RMS=0.079 (target=0.015)
step 010: RMS=0.057 (target=0.015)
step 015: RMS=0.047 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.029 (target=0.015)
step 035: RMS=0.025 (target=0.015)
step 040: RMS=0.021 (target=0.015)
step 045: RMS=0.019 (target=0.015)
step 050: RMS=0.018 (target=0.015)
step 055: RMS=0.016 (target=0.015)
step 060: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.7 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
- 207 vertices thresholded to be in k1 ~ [-0.22 0.45], k2 ~ [-0.25 0.07]
- total integrated curvature = 0.541*4pi (6.803) --> 0 handles
- ICI = 1.6, FI = 9.9, variation=170.305
- 178 vertices thresholded to be in [-0.03 0.02]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 137 vertices thresholded to be in [-0.14 0.14]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.020
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 18:19:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub002 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 [ sub002/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 [ 297 ]
- Gb_filter = 0
- WARN: S lookup min: -0.141974
- WARN: S explicit min: 0.000000 vertex = 523
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 18:19:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 0.270...
- 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 %20.81
- pass 1: epoch 2 of 3 starting distance error %20.79
- unfolding complete - removing small folds...
- starting distance error %20.68
- removing remaining folds...
- final distance error %20.70
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.15 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 19:28:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 0.613
- curvature mean = 0.042, std = 0.935
- curvature mean = 0.024, std = 0.847
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 406375.4, tmin=1.3426
- d=32.00 min @ (-8.00, -8.00, 0.00) sse = 292306.6, tmin=2.6693
- d=16.00 min @ (0.00, 0.00, -4.00) sse = 277955.5, tmin=4.0334
- d=8.00 min @ (2.00, 0.00, 0.00) sse = 273601.4, tmin=5.4351
- d=4.00 min @ (-1.00, -1.00, 1.00) sse = 270771.8, tmin=6.8509
- d=1.00 min @ (0.25, 0.25, 0.00) sse = 270626.5, tmin=9.7036
- d=0.50 min @ (0.00, 0.00, 0.12) sse = 270599.8, tmin=11.0924
- 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 11.09 min
- curvature mean = 0.008, std = 0.940
- curvature mean = 0.012, std = 0.934
- curvature mean = 0.004, std = 0.949
- curvature mean = 0.006, std = 0.969
- curvature mean = 0.001, std = 0.950
- curvature mean = 0.002, std = 0.986
- 2 Reading smoothwm
- curvature mean = -0.021, std = 0.388
- curvature mean = 0.003, std = 0.066
- curvature mean = 0.049, std = 0.235
- curvature mean = 0.003, std = 0.079
- curvature mean = 0.021, std = 0.375
- curvature mean = 0.003, std = 0.084
- curvature mean = 0.010, std = 0.483
- curvature mean = 0.003, std = 0.087
- curvature mean = 0.003, std = 0.584
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 20:02:00 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 20:02:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 20:02:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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...
- 1305 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3454 changed, 162178 examined...
- 001: 789 changed, 14622 examined...
- 002: 188 changed, 4322 examined...
- 003: 63 changed, 1074 examined...
- 004: 26 changed, 386 examined...
- 005: 15 changed, 153 examined...
- 006: 9 changed, 93 examined...
- 007: 3 changed, 50 examined...
- 008: 0 changed, 17 examined...
- 230 labels changed using aseg
- 000: 143 total segments, 97 labels (308 vertices) changed
- 001: 46 total segments, 1 labels (3 vertices) changed
- 002: 45 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 49 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 2163 vertices marked for relabeling...
- 2163 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 14 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 20:03:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub002 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/sub002/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- 20389 bright wm thresholded.
- 326 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.orig...
- computing class statistics...
- border white: 305608 voxels (1.82%)
- border gray 333888 voxels (1.99%)
- WM (92.0): 93.4 +- 9.7 [70.0 --> 110.0]
- GM (76.0) : 74.6 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 48.3 (was 70)
- setting MAX_BORDER_WHITE to 114.7 (was 105)
- setting MIN_BORDER_WHITE to 61.0 (was 85)
- setting MAX_CSF to 35.6 (was 40)
- setting MAX_GRAY to 95.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 54.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 22.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=61
- mean inside = 92.7, mean outside = 69.6
- 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/sub002/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.02-->2.48) (max @ vno 117773 --> 118787)
- face area 0.28 +- 0.12 (0.00-->2.11)
- mean absolute distance = 0.77 +- 0.96
- 3703 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 4 with 12 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- deleting segment 6 with 25 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- mean border=73.1, 146 (146) missing vertices, mean dist 0.3 [0.7 (%29.1)->0.8 (%70.9))]
- %61 local maxima, %34 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 (0.10-->3.38) (max @ vno 112452 --> 112451)
- face area 0.28 +- 0.13 (0.00-->1.76)
- mean absolute distance = 0.38 +- 0.56
- 3451 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8277498.0, rms=13.32
- 001: dt: 0.5000, sse=8104297.0, rms=9.538 (0.000%)
- 002: dt: 0.5000, sse=8189057.0, rms=7.204 (0.000%)
- 003: dt: 0.5000, sse=8438055.0, rms=5.718 (0.000%)
- 004: dt: 0.5000, sse=8621839.0, rms=4.844 (0.000%)
- 005: dt: 0.5000, sse=8859667.0, rms=4.370 (0.000%)
- 006: dt: 0.5000, sse=8931330.0, rms=4.155 (0.000%)
- 007: dt: 0.5000, sse=9015885.0, rms=4.034 (0.000%)
- 008: dt: 0.5000, sse=9004967.0, rms=3.978 (0.000%)
- rms = 3.93, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=8989411.0, rms=3.929 (0.000%)
- 010: dt: 0.2500, sse=5421008.5, rms=2.666 (0.000%)
- 011: dt: 0.2500, sse=4922914.0, rms=2.224 (0.000%)
- 012: dt: 0.2500, sse=4626976.0, rms=2.112 (0.000%)
- 013: dt: 0.2500, sse=4542123.0, rms=2.024 (0.000%)
- rms = 1.99, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4450310.0, rms=1.994 (0.000%)
- 015: dt: 0.1250, sse=4289231.5, rms=1.853 (0.000%)
- rms = 1.84, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4247387.5, rms=1.838 (0.000%)
- positioning took 2.5 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
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- deleting segment 5 with 62 points - only 29.03% unknown
- deleting segment 6 with 14 points - only 0.00% unknown
- deleting segment 7 with 11 points - only 0.00% unknown
- deleting segment 8 with 29 points - only 0.00% unknown
- deleting segment 9 with 13 points - only 0.00% unknown
- mean border=78.3, 112 (47) missing vertices, mean dist -0.3 [0.4 (%79.8)->0.2 (%20.2))]
- %78 local maxima, %18 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-->3.74) (max @ vno 106914 --> 105889)
- face area 0.35 +- 0.16 (0.00-->2.19)
- mean absolute distance = 0.23 +- 0.32
- 3010 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5700380.0, rms=6.74
- 017: dt: 0.5000, sse=5576232.5, rms=4.227 (0.000%)
- rms = 4.24, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5080995.5, rms=3.234 (0.000%)
- 019: dt: 0.2500, sse=4820064.5, rms=2.389 (0.000%)
- 020: dt: 0.2500, sse=4724833.0, rms=1.903 (0.000%)
- 021: dt: 0.2500, sse=4671011.0, rms=1.772 (0.000%)
- 022: dt: 0.2500, sse=4595735.0, rms=1.664 (0.000%)
- rms = 1.63, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4587611.5, rms=1.630 (0.000%)
- 024: dt: 0.1250, sse=4469250.5, rms=1.507 (0.000%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4432582.5, rms=1.497 (0.000%)
- positioning took 1.5 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 5 points - only 0.00% unknown
- deleting segment 3 with 136 points - only 58.82% unknown
- deleting segment 4 with 12 points - only 0.00% unknown
- deleting segment 5 with 11 points - only 0.00% unknown
- deleting segment 6 with 29 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- mean border=81.8, 108 (27) missing vertices, mean dist -0.2 [0.2 (%77.5)->0.2 (%22.5))]
- %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.07-->4.01) (max @ vno 106914 --> 105889)
- face area 0.34 +- 0.16 (0.00-->2.26)
- mean absolute distance = 0.17 +- 0.25
- 2787 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4956790.0, rms=4.50
- 026: dt: 0.5000, sse=5243048.5, rms=3.726 (0.000%)
- rms = 3.99, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4750395.5, rms=2.356 (0.000%)
- 028: dt: 0.2500, sse=4629788.5, rms=1.850 (0.000%)
- 029: dt: 0.2500, sse=4657395.0, rms=1.542 (0.000%)
- rms = 1.56, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4597971.0, rms=1.451 (0.000%)
- 031: dt: 0.1250, sse=4521950.5, rms=1.325 (0.000%)
- rms = 1.32, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4484707.0, rms=1.318 (0.000%)
- positioning took 1.2 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 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 136 points - only 58.82% unknown
- deleting segment 4 with 10 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 11 points - only 0.00% unknown
- deleting segment 7 with 33 points - only 0.00% unknown
- deleting segment 8 with 13 points - only 0.00% unknown
- mean border=82.8, 123 (22) missing vertices, mean dist -0.0 [0.2 (%58.1)->0.2 (%41.9))]
- %91 local maxima, % 5 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=4521456.0, rms=1.80
- rms = 2.50, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4617454.0, rms=1.172 (0.000%)
- 034: dt: 0.2500, sse=4796951.5, rms=0.995 (0.000%)
- rms = 1.00, time step reduction 2 of 3 to 0.125...
- rms = 0.99, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4796746.5, rms=0.987 (0.000%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=51.0, 144 (144) missing vertices, mean dist 1.9 [0.1 (%0.0)->2.2 (%100.0))]
- %21 local maxima, %61 large gradients and %14 min vals, 1237 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=33542884.0, rms=31.33
- 001: dt: 0.5000, sse=24071146.0, rms=26.008 (0.000%)
- 002: dt: 0.5000, sse=17442914.0, rms=21.547 (0.000%)
- 003: dt: 0.5000, sse=13096878.0, rms=17.941 (0.000%)
- 004: dt: 0.5000, sse=10597893.0, rms=15.121 (0.000%)
- 005: dt: 0.5000, sse=9240971.0, rms=12.974 (0.000%)
- 006: dt: 0.5000, sse=8527073.0, rms=11.354 (0.000%)
- 007: dt: 0.5000, sse=8051078.5, rms=9.951 (0.000%)
- 008: dt: 0.5000, sse=7681486.0, rms=8.633 (0.000%)
- 009: dt: 0.5000, sse=7483358.5, rms=7.368 (0.000%)
- 010: dt: 0.5000, sse=7441162.5, rms=6.254 (0.000%)
- 011: dt: 0.5000, sse=7532366.0, rms=5.404 (0.000%)
- 012: dt: 0.5000, sse=7677448.5, rms=4.865 (0.000%)
- 013: dt: 0.5000, sse=7882003.5, rms=4.562 (0.000%)
- 014: dt: 0.5000, sse=7996728.5, rms=4.379 (0.000%)
- 015: dt: 0.5000, sse=8083462.0, rms=4.260 (0.000%)
- 016: dt: 0.5000, sse=8105952.5, rms=4.171 (0.000%)
- 017: dt: 0.5000, sse=8170469.0, rms=4.111 (0.000%)
- rms = 4.07, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=8189036.0, rms=4.068 (0.000%)
- 019: dt: 0.2500, sse=5352816.0, rms=3.085 (0.000%)
- 020: dt: 0.2500, sse=5082524.5, rms=2.815 (0.000%)
- 021: dt: 0.2500, sse=4904897.0, rms=2.763 (0.000%)
- rms = 2.74, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4858443.0, rms=2.738 (0.000%)
- 023: dt: 0.1250, sse=4617195.0, rms=2.564 (0.000%)
- rms = 2.54, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4586460.0, rms=2.541 (0.000%)
- positioning took 3.5 minutes
- mean border=47.4, 504 (17) missing vertices, mean dist 0.2 [0.2 (%40.3)->0.5 (%59.7))]
- %44 local maxima, %41 large gradients and %10 min vals, 386 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=5666737.0, rms=5.73
- 025: dt: 0.5000, sse=5772666.5, rms=4.367 (0.000%)
- rms = 4.35, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.5000, sse=7566291.5, rms=4.347 (0.000%)
- 027: dt: 0.2500, sse=5525399.5, rms=3.152 (0.000%)
- 028: dt: 0.2500, sse=5577510.0, rms=2.825 (0.000%)
- 029: dt: 0.2500, sse=5397909.5, rms=2.774 (0.000%)
- 030: dt: 0.2500, sse=5470158.5, rms=2.702 (0.000%)
- rms = 2.70, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.1250, sse=5343195.0, rms=2.603 (0.000%)
- 032: dt: 0.1250, sse=5151511.5, rms=2.459 (0.000%)
- rms = 2.43, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=5108980.0, rms=2.430 (0.000%)
- positioning took 1.4 minutes
- mean border=44.4, 662 (11) missing vertices, mean dist 0.2 [0.2 (%32.8)->0.3 (%67.2))]
- %64 local maxima, %22 large gradients and %10 min vals, 446 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=5586529.5, rms=4.51
- 034: dt: 0.5000, sse=5823650.0, rms=4.289 (0.000%)
- rms = 4.31, time step reduction 1 of 3 to 0.250...
- 035: dt: 0.2500, sse=5343568.5, rms=3.145 (0.000%)
- 036: dt: 0.2500, sse=5491674.5, rms=2.678 (0.000%)
- 037: dt: 0.2500, sse=5479107.5, rms=2.588 (0.000%)
- rms = 2.56, time step reduction 2 of 3 to 0.125...
- 038: dt: 0.2500, sse=5516970.5, rms=2.556 (0.000%)
- 039: dt: 0.1250, sse=5265964.5, rms=2.310 (0.000%)
- rms = 2.27, time step reduction 3 of 3 to 0.062...
- 040: dt: 0.1250, sse=5245404.5, rms=2.272 (0.000%)
- positioning took 1.1 minutes
- mean border=43.1, 1454 (5) missing vertices, mean dist 0.1 [0.2 (%43.2)->0.2 (%56.8))]
- %67 local maxima, %18 large gradients and %10 min vals, 294 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/sub002/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=5316321.5, rms=2.76
- rms = 3.84, time step reduction 1 of 3 to 0.250...
- 041: dt: 0.2500, sse=5160718.5, rms=2.365 (0.000%)
- 042: dt: 0.2500, sse=5316253.5, rms=2.295 (0.000%)
- rms = 2.30, time step reduction 2 of 3 to 0.125...
- rms = 2.25, time step reduction 3 of 3 to 0.062...
- 043: dt: 0.1250, sse=5266903.0, rms=2.252 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.area.pial
- vertex spacing 1.00 +- 0.41 (0.07-->7.07) (max @ vno 111435 --> 111419)
- face area 0.40 +- 0.29 (0.00-->4.99)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 162178 vertices processed
- 25000 of 162178 vertices processed
- 50000 of 162178 vertices processed
- 75000 of 162178 vertices processed
- 100000 of 162178 vertices processed
- 125000 of 162178 vertices processed
- 150000 of 162178 vertices processed
- 0 of 162178 vertices processed
- 25000 of 162178 vertices processed
- 50000 of 162178 vertices processed
- 75000 of 162178 vertices processed
- 100000 of 162178 vertices processed
- 125000 of 162178 vertices processed
- 150000 of 162178 vertices processed
- thickness calculation complete, 557:854 truncations.
- 44192 vertices at 0 distance
- 120328 vertices at 1 distance
- 98971 vertices at 2 distance
- 35103 vertices at 3 distance
- 9118 vertices at 4 distance
- 2429 vertices at 5 distance
- 814 vertices at 6 distance
- 283 vertices at 7 distance
- 102 vertices at 8 distance
- 51 vertices at 9 distance
- 27 vertices at 10 distance
- 19 vertices at 11 distance
- 17 vertices at 12 distance
- 8 vertices at 13 distance
- 14 vertices at 14 distance
- 12 vertices at 15 distance
- 10 vertices at 16 distance
- 6 vertices at 17 distance
- 0 vertices at 18 distance
- 1 vertices at 19 distance
- 3 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.thickness
- positioning took 17.0 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 20:20:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 20:20:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- pctsurfcon --s sub002 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/pctsurfcon.log
- Thu Aug 8 20:20:22 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.wm.mgh --regheader sub002 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 125798
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.wm.mgh
- Dim: 162178 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.gm.mgh --projfrac 0.3 --regheader sub002 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 144480
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.gm.mgh
- Dim: 162178 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.w-g.pct.mgh --annot sub002 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/lh.w-g.pct.mgh --annot sub002 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/lh.w-g.pct.mgh
- Vertex Area is 0.660581 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1908 1358.553
- 2 1002 caudalanteriorcingulate 1237 841.711
- 3 1003 caudalmiddlefrontal 3707 2429.536
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2490 1644.200
- 6 1006 entorhinal 570 388.561
- 7 1007 fusiform 5387 3586.849
- 8 1008 inferiorparietal 8738 5797.738
- 9 1009 inferiortemporal 6203 4139.783
- 10 1010 isthmuscingulate 2304 1469.004
- 11 1011 lateraloccipital 7544 4960.165
- 12 1012 lateralorbitofrontal 4373 2897.055
- 13 1013 lingual 4490 2990.144
- 14 1014 medialorbitofrontal 3123 2057.696
- 15 1015 middletemporal 6067 4163.659
- 16 1016 parahippocampal 1546 1015.344
- 17 1017 paracentral 2075 1301.509
- 18 1018 parsopercularis 2742 1860.310
- 19 1019 parsorbitalis 1178 782.502
- 20 1020 parstriangularis 2322 1553.732
- 21 1021 pericalcarine 2216 1526.616
- 22 1022 postcentral 7463 4733.478
- 23 1023 posteriorcingulate 1929 1285.999
- 24 1024 precentral 9202 5651.326
- 25 1025 precuneus 8368 5567.865
- 26 1026 rostralanteriorcingulate 1594 1070.627
- 27 1027 rostralmiddlefrontal 10672 7247.876
- 28 1028 superiorfrontal 13407 9095.433
- 29 1029 superiorparietal 9674 6236.878
- 30 1030 superiortemporal 7245 4841.190
- 31 1031 supramarginal 8068 5468.552
- 32 1032 frontalpole 419 287.002
- 33 1033 temporalpole 832 586.120
- 34 1034 transversetemporal 732 440.409
- 35 1035 insula 3766 2476.238
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 20:20:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 1908 1359 3338 2.408 0.420 0.126 0.033 24 2.7 bankssts
- 1237 842 2268 2.414 0.770 0.141 0.037 21 1.9 caudalanteriorcingulate
- 3707 2430 6447 2.487 0.490 0.117 0.035 35 5.4 caudalmiddlefrontal
- 2490 1644 4161 2.151 0.451 0.165 0.059 49 6.1 cuneus
- 570 389 1979 3.623 0.793 0.159 0.077 11 2.0 entorhinal
- 5387 3587 11544 2.765 0.711 0.139 0.052 91 11.1 fusiform
- 8738 5798 14900 2.336 0.394 0.136 0.050 148 17.4 inferiorparietal
- 6203 4140 12913 2.690 0.725 0.154 0.061 129 15.1 inferiortemporal
- 2304 1469 4092 2.432 0.877 0.155 0.090 47 7.1 isthmuscingulate
- 7544 4960 11851 2.100 0.395 0.152 0.056 149 16.9 lateraloccipital
- 4373 2897 8064 2.481 0.603 0.160 0.073 124 13.9 lateralorbitofrontal
- 4490 2990 7097 2.150 0.535 0.155 0.061 85 11.2 lingual
- 3123 2058 5175 2.155 0.810 0.147 0.068 83 9.4 medialorbitofrontal
- 6067 4164 14504 2.816 0.571 0.145 0.057 140 15.3 middletemporal
- 1546 1015 2886 2.404 0.613 0.106 0.035 13 2.4 parahippocampal
- 2075 1302 3416 2.361 0.720 0.126 0.042 29 3.8 paracentral
- 2742 1860 5691 2.723 0.454 0.127 0.037 31 4.2 parsopercularis
- 1178 783 2698 2.574 0.580 0.158 0.055 25 2.6 parsorbitalis
- 2322 1554 4236 2.438 0.418 0.138 0.044 33 4.2 parstriangularis
- 2216 1527 2696 1.821 0.465 0.141 0.067 37 5.5 pericalcarine
- 7463 4733 11214 2.078 0.542 0.126 0.041 96 12.4 postcentral
- 1929 1286 3528 2.624 0.549 0.154 0.059 43 4.5 posteriorcingulate
- 9202 5651 16225 2.629 0.551 0.118 0.044 105 17.1 precentral
- 8368 5568 14479 2.422 0.480 0.131 0.044 114 14.0 precuneus
- 1594 1071 3090 2.436 0.804 0.180 0.091 47 5.4 rostralanteriorcingulate
- 10672 7248 18731 2.316 0.499 0.152 0.056 196 23.3 rostralmiddlefrontal
- 13407 9095 26583 2.526 0.607 0.146 0.083 1763 51.0 superiorfrontal
- 9674 6237 14961 2.180 0.418 0.125 0.035 113 13.7 superiorparietal
- 7245 4841 15521 2.886 0.584 0.124 0.092 242 13.7 superiortemporal
- 8068 5469 14809 2.437 0.439 0.139 0.047 134 14.3 supramarginal
- 419 287 979 2.544 0.519 0.194 0.071 12 1.3 frontalpole
- 832 586 2930 3.707 0.802 0.156 0.075 14 2.5 temporalpole
- 732 440 1256 2.497 0.307 0.129 0.041 9 1.3 transversetemporal
- 3766 2476 7768 3.009 0.826 0.124 0.054 51 7.3 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 20:21:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs...
- reading color table from GCSA file....
- average std = 3.9 0.2 using min determinant for regularization = 0.000
- 0 singular and 1066 ill-conditioned covariance matrices regularized
- input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 19 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10727 changed, 162178 examined...
- 001: 2554 changed, 41118 examined...
- 002: 759 changed, 13329 examined...
- 003: 341 changed, 4318 examined...
- 004: 152 changed, 1954 examined...
- 005: 85 changed, 863 examined...
- 006: 55 changed, 466 examined...
- 007: 33 changed, 310 examined...
- 008: 19 changed, 177 examined...
- 009: 6 changed, 99 examined...
- 010: 3 changed, 36 examined...
- 011: 1 changed, 16 examined...
- 012: 0 changed, 5 examined...
- 12 labels changed using aseg
- 000: 337 total segments, 249 labels (2892 vertices) changed
- 001: 101 total segments, 13 labels (58 vertices) changed
- 002: 88 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 148 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1262 vertices marked for relabeling...
- 1262 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 23 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 20:22:26 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 1443 975 2438 2.283 0.512 0.168 0.062 30 3.6 G_and_S_frontomargin
- 1499 1010 2478 2.151 0.427 0.147 0.049 23 2.8 G_and_S_occipital_inf
- 1456 842 2306 2.289 0.731 0.131 0.050 29 3.3 G_and_S_paracentral
- 1954 1275 3341 2.385 0.611 0.142 0.045 33 3.4 G_and_S_subcentral
- 1006 699 2118 2.369 0.516 0.184 0.077 30 3.0 G_and_S_transv_frontopol
- 2522 1742 4569 2.426 0.718 0.147 0.055 44 5.5 G_and_S_cingul-Ant
- 1769 1232 3487 2.599 0.614 0.131 0.036 22 2.6 G_and_S_cingul-Mid-Ant
- 1530 1051 2810 2.570 0.470 0.135 0.045 23 2.8 G_and_S_cingul-Mid-Post
- 865 550 2114 3.085 0.533 0.171 0.063 20 2.3 G_cingul-Post-dorsal
- 505 315 753 1.985 0.832 0.155 0.157 10 1.3 G_cingul-Post-ventral
- 2221 1463 3913 2.161 0.491 0.175 0.071 55 6.9 G_cuneus
- 1521 1029 4025 2.937 0.379 0.143 0.052 25 3.0 G_front_inf-Opercular
- 575 376 1243 2.662 0.473 0.151 0.058 14 1.3 G_front_inf-Orbital
- 1477 969 3174 2.530 0.408 0.157 0.051 27 3.2 G_front_inf-Triangul
- 5359 3547 11115 2.491 0.509 0.154 0.060 107 12.9 G_front_middle
- 9199 6171 20236 2.636 0.644 0.160 0.108 1727 45.9 G_front_sup
- 578 361 1369 3.301 0.768 0.124 0.045 8 1.0 G_Ins_lg_and_S_cent_ins
- 859 578 2692 3.636 0.825 0.162 0.112 26 3.0 G_insular_short
- 2652 1659 5248 2.429 0.366 0.169 0.076 80 8.1 G_occipital_middle
- 1645 1049 2761 2.154 0.427 0.149 0.052 32 3.5 G_occipital_sup
- 2043 1322 5176 2.994 0.624 0.157 0.061 49 5.0 G_oc-temp_lat-fusifor
- 3020 1949 5091 2.108 0.568 0.163 0.072 61 8.8 G_oc-temp_med-Lingual
- 1392 893 3697 3.150 0.911 0.122 0.044 16 2.5 G_oc-temp_med-Parahip
- 3282 2178 7192 2.550 0.630 0.170 0.082 110 11.9 G_orbital
- 3038 2029 5831 2.361 0.403 0.144 0.052 61 6.6 G_pariet_inf-Angular
- 4341 2946 9366 2.574 0.425 0.151 0.058 101 9.2 G_pariet_inf-Supramar
- 4170 2663 7674 2.322 0.408 0.135 0.041 63 6.9 G_parietal_sup
- 2814 1691 4819 2.238 0.477 0.132 0.052 44 5.6 G_postcentral
- 3727 2133 7748 2.848 0.474 0.121 0.057 59 9.1 G_precentral
- 3655 2432 7768 2.532 0.529 0.147 0.057 70 7.6 G_precuneus
- 1075 707 2076 2.149 0.621 0.191 0.092 45 4.3 G_rectus
- 674 428 1331 2.746 1.005 0.117 0.095 25 2.9 G_subcallosal
- 500 287 994 2.628 0.258 0.132 0.045 7 0.9 G_temp_sup-G_T_transv
- 2477 1615 6914 3.139 0.485 0.143 0.199 193 5.8 G_temp_sup-Lateral
- 853 579 2295 3.572 0.550 0.132 0.083 15 3.1 G_temp_sup-Plan_polar
- 1514 1062 2916 2.481 0.440 0.131 0.035 19 2.3 G_temp_sup-Plan_tempo
- 3393 2265 8846 2.912 0.753 0.173 0.080 97 10.3 G_temporal_inf
- 4130 2822 10653 2.822 0.572 0.159 0.070 125 12.9 G_temporal_middle
- 358 237 453 2.270 0.495 0.105 0.029 2 0.4 Lat_Fis-ant-Horizont
- 304 224 503 2.559 0.421 0.112 0.028 3 0.3 Lat_Fis-ant-Vertical
- 1619 1072 2223 2.377 0.378 0.121 0.037 14 2.5 Lat_Fis-post
- 2181 1451 3251 1.940 0.374 0.168 0.073 56 6.4 Pole_occipital
- 2103 1463 6747 3.293 0.887 0.174 0.091 49 7.4 Pole_temporal
- 2673 1862 3543 2.099 0.653 0.142 0.049 41 5.0 S_calcarine
- 3348 2175 3826 1.939 0.593 0.113 0.031 21 4.7 S_central
- 1269 828 2042 2.274 0.493 0.124 0.047 16 2.3 S_cingul-Marginalis
- 485 333 841 2.894 0.535 0.122 0.031 3 0.6 S_circular_insula_ant
- 1526 996 2439 2.747 0.573 0.089 0.022 6 1.4 S_circular_insula_inf
- 2116 1423 3234 2.542 0.407 0.113 0.031 14 2.7 S_circular_insula_sup
- 796 546 1487 2.753 0.610 0.136 0.042 10 1.4 S_collat_transv_ant
- 427 285 509 2.007 0.365 0.130 0.032 3 0.6 S_collat_transv_post
- 2671 1824 3950 2.296 0.425 0.121 0.033 24 3.7 S_front_inf
- 2306 1560 3336 2.083 0.469 0.132 0.042 28 3.7 S_front_middle
- 3117 2100 4879 2.319 0.443 0.110 0.032 24 3.8 S_front_sup
- 805 525 1006 2.254 0.333 0.119 0.029 6 1.0 S_interm_prim-Jensen
- 3767 2494 4789 2.094 0.325 0.112 0.026 28 4.1 S_intrapariet_and_P_trans
- 1050 717 1271 1.938 0.358 0.127 0.031 9 1.3 S_oc_middle_and_Lunatus
- 1788 1180 2352 2.117 0.329 0.109 0.025 12 1.9 S_oc_sup_and_transversal
- 705 472 849 2.039 0.278 0.115 0.027 5 0.8 S_occipital_ant
- 1244 828 1671 2.200 0.433 0.108 0.031 10 1.6 S_oc-temp_lat
- 2815 1946 4287 2.408 0.475 0.115 0.031 21 3.9 S_oc-temp_med_and_Lingual
- 385 268 553 2.453 0.447 0.127 0.041 3 0.6 S_orbital_lateral
- 808 548 1246 2.304 0.796 0.128 0.035 7 1.2 S_orbital_med-olfact
- 1378 924 2144 2.277 0.526 0.158 0.061 30 3.2 S_orbital-H_Shaped
- 2739 1786 3678 2.187 0.418 0.115 0.040 27 3.6 S_parieto_occipital
- 1704 1066 1845 2.014 0.709 0.160 0.078 45 5.6 S_pericallosal
- 3894 2570 4985 2.112 0.446 0.118 0.033 33 5.3 S_postcentral
- 2030 1364 3033 2.585 0.427 0.109 0.025 13 2.2 S_precentral-inf-part
- 1679 1136 2391 2.295 0.414 0.109 0.025 11 1.8 S_precentral-sup-part
- 933 615 1293 1.933 0.732 0.137 0.053 14 2.1 S_suborbital
- 1918 1305 3083 2.479 0.435 0.125 0.035 19 2.8 S_subparietal
- 2304 1543 3455 2.482 0.626 0.129 0.039 26 3.8 S_temporal_inf
- 7184 4898 11561 2.442 0.430 0.120 0.035 76 9.7 S_temporal_sup
- 429 297 696 2.605 0.379 0.113 0.025 2 0.5 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 20:22:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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...
- 1018 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3257 changed, 162178 examined...
- 001: 763 changed, 13667 examined...
- 002: 198 changed, 4102 examined...
- 003: 79 changed, 1213 examined...
- 004: 39 changed, 463 examined...
- 005: 20 changed, 244 examined...
- 006: 6 changed, 119 examined...
- 007: 4 changed, 39 examined...
- 008: 2 changed, 27 examined...
- 009: 2 changed, 13 examined...
- 010: 2 changed, 12 examined...
- 011: 0 changed, 13 examined...
- 131 labels changed using aseg
- 000: 80 total segments, 47 labels (552 vertices) changed
- 001: 35 total segments, 2 labels (4 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 45 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 842 vertices marked for relabeling...
- 842 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 16 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 20:24:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 2117 1450 4172 2.600 0.692 0.135 0.037 31 3.2 caudalanteriorcingulate
- 3793 2479 6653 2.500 0.485 0.118 0.035 36 5.7 caudalmiddlefrontal
- 3548 2344 5746 2.153 0.442 0.149 0.050 60 7.4 cuneus
- 519 354 1868 3.760 0.767 0.150 0.056 7 1.1 entorhinal
- 4992 3319 10173 2.721 0.681 0.133 0.044 74 9.3 fusiform
- 8311 5508 14130 2.322 0.392 0.137 0.050 144 17.0 inferiorparietal
- 6272 4181 13685 2.734 0.756 0.159 0.068 144 16.8 inferiortemporal
- 2301 1468 4109 2.431 0.877 0.155 0.091 48 7.1 isthmuscingulate
- 7732 5087 12054 2.088 0.388 0.152 0.057 153 17.2 lateraloccipital
- 4894 3210 9081 2.508 0.685 0.164 0.076 142 15.9 lateralorbitofrontal
- 4489 2986 7083 2.148 0.535 0.156 0.061 85 11.2 lingual
- 2481 1638 4159 2.080 0.709 0.158 0.075 77 8.5 medialorbitofrontal
- 8003 5494 17839 2.734 0.557 0.142 0.054 167 18.6 middletemporal
- 1538 1010 2841 2.391 0.596 0.106 0.035 12 2.4 parahippocampal
- 2467 1564 4369 2.478 0.733 0.128 0.045 36 4.8 paracentral
- 2462 1663 5118 2.754 0.454 0.126 0.037 26 3.8 parsopercularis
- 1342 902 2928 2.689 0.477 0.139 0.048 20 2.5 parsorbitalis
- 2850 1922 5167 2.418 0.425 0.141 0.043 43 5.2 parstriangularis
- 2226 1528 2708 1.826 0.470 0.141 0.068 37 5.5 pericalcarine
- 8325 5296 12367 2.096 0.546 0.127 0.042 105 13.8 postcentral
- 2152 1435 3867 2.620 0.534 0.151 0.057 45 4.9 posteriorcingulate
- 9025 5546 15843 2.628 0.552 0.118 0.044 104 17.0 precentral
- 8041 5338 14146 2.438 0.480 0.134 0.045 114 14.0 precuneus
- 2102 1411 3766 2.359 0.791 0.168 0.082 52 6.3 rostralanteriorcingulate
- 7648 5180 13626 2.323 0.507 0.148 0.051 131 15.7 rostralmiddlefrontal
- 14727 10003 28549 2.447 0.600 0.149 0.084 1804 54.8 superiorfrontal
- 7867 5076 12219 2.183 0.397 0.122 0.033 87 10.5 superiorparietal
- 9442 6377 21026 2.907 0.660 0.128 0.084 275 18.4 superiortemporal
- 7873 5340 14427 2.438 0.440 0.138 0.047 129 13.8 supramarginal
- 733 445 1262 2.502 0.310 0.129 0.041 8 1.3 transversetemporal
- 3319 2198 7050 3.008 0.817 0.122 0.053 45 6.1 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 20:24:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 2 found - 2 modified | TOTAL: 2
- pass 2 (xy+): 0 found - 2 modified | TOTAL: 2
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 2
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 3
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 3
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 4
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 4
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 4
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 7
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 7
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 2 found - 2 modified | TOTAL: 2
- pass 2 (--): 0 found - 2 modified | TOTAL: 2
- pass 1 (-+): 1 found - 1 modified | TOTAL: 3
- pass 2 (-+): 0 found - 1 modified | TOTAL: 3
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 10 (out of 314383: 0.003181)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 40: 2425 vertices, 2588 faces
- slice 50: 9338 vertices, 9682 faces
- slice 60: 19850 vertices, 20243 faces
- slice 70: 32136 vertices, 32562 faces
- slice 80: 45543 vertices, 45938 faces
- slice 90: 58145 vertices, 58605 faces
- slice 100: 70944 vertices, 71360 faces
- slice 110: 82751 vertices, 83163 faces
- slice 120: 94673 vertices, 95112 faces
- slice 130: 106444 vertices, 106869 faces
- slice 140: 117806 vertices, 118215 faces
- slice 150: 128578 vertices, 128945 faces
- slice 160: 137412 vertices, 137712 faces
- slice 170: 145518 vertices, 145783 faces
- slice 180: 152727 vertices, 152983 faces
- slice 190: 158448 vertices, 158645 faces
- slice 200: 162265 vertices, 162316 faces
- slice 210: 162428 vertices, 162448 faces
- slice 220: 162428 vertices, 162448 faces
- slice 230: 162428 vertices, 162448 faces
- slice 240: 162428 vertices, 162448 faces
- slice 250: 162428 vertices, 162448 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...
- 162428 voxel in cpt #1: X=-20 [v=162428,e=487344,f=324896] located at (30.741030, -17.895498, 39.739590)
- For the whole surface: X=-20 [v=162428,e=487344,f=324896]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 20:24:59 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 20:25:04 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- avg radius = 50.0 mm, total surface area = 86209 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=0.053 (target=0.015)
step 015: RMS=0.045 (target=0.015)
step 020: RMS=0.038 (target=0.015)
step 025: RMS=0.033 (target=0.015)
step 030: RMS=0.030 (target=0.015)
step 035: RMS=0.027 (target=0.015)
step 040: RMS=0.026 (target=0.015)
step 045: RMS=0.024 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.023 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 20:25:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 0.91 +- 0.54 (0.00-->5.95) (max @ vno 123027 --> 123028)
- face area 0.02 +- 0.03 (-0.18-->0.54)
- scaling brain by 0.292...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.202, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.942, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.382, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.647, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.811, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.915, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.991, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.051, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.106, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.159, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.213, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.270, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.330, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.395, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.464, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.539, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.618, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.703, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.793, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.889, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.990, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.096, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.207, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.323, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.444, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.570, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.701, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.837, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.978, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.125, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.276, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.431, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.592, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.757, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.927, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.101, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.280, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.464, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.652, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.844, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.041, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.242, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.447, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.657, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.871, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.090, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.313, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.540, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.771, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.007, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.247, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.491, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.739, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.992, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.248, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.509, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.774, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.043, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.316, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.593, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.874, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 19353.82
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
- epoch 2 (K=40.0), pass 1, starting sse = 3355.26
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00003
- epoch 3 (K=160.0), pass 1, starting sse = 369.37
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.09/12 = 0.00788
- epoch 4 (K=640.0), pass 1, starting sse = 23.43
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.23/20 = 0.01128
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.13 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 20:33:25 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/sub002/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub002 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=-20 (nv=162428, nf=324896, ne=487344, g=11)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 2074 ambiguous faces found in tessellation
- segmenting defects...
- 27 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 17 into 16
- 26 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8100 (-4.9050)
- -vertex loglikelihood: -6.6243 (-3.3121)
- -normal dot loglikelihood: -3.6536 (-3.6536)
- -quad curv loglikelihood: -6.3507 (-3.1753)
- Total Loglikelihood : -26.4385
- CORRECTING DEFECT 0 (vertices=6, convex hull=20)
- After retessellation of defect 0, euler #=-24 (161140,482924,321760) : difference with theory (-23) = 1
- CORRECTING DEFECT 1 (vertices=26, convex hull=37)
- After retessellation of defect 1, euler #=-23 (161146,482954,321785) : difference with theory (-22) = 1
- CORRECTING DEFECT 2 (vertices=28, convex hull=34)
- After retessellation of defect 2, euler #=-22 (161149,482976,321805) : difference with theory (-21) = 1
- CORRECTING DEFECT 3 (vertices=110, convex hull=83)
- After retessellation of defect 3, euler #=-21 (161166,483064,321877) : difference with theory (-20) = 1
- CORRECTING DEFECT 4 (vertices=14, convex hull=28)
- After retessellation of defect 4, euler #=-20 (161170,483084,321894) : difference with theory (-19) = 1
- CORRECTING DEFECT 5 (vertices=33, convex hull=54)
- After retessellation of defect 5, euler #=-19 (161187,483156,321950) : difference with theory (-18) = 1
- CORRECTING DEFECT 6 (vertices=40, convex hull=81)
- After retessellation of defect 6, euler #=-18 (161195,483211,321998) : difference with theory (-17) = 1
- CORRECTING DEFECT 7 (vertices=12, convex hull=18)
- After retessellation of defect 7, euler #=-17 (161196,483217,322004) : difference with theory (-16) = 1
- CORRECTING DEFECT 8 (vertices=13, convex hull=14)
- After retessellation of defect 8, euler #=-16 (161199,483230,322015) : difference with theory (-15) = 1
- CORRECTING DEFECT 9 (vertices=263, convex hull=105)
- After retessellation of defect 9, euler #=-15 (161210,483311,322086) : difference with theory (-14) = 1
- CORRECTING DEFECT 10 (vertices=5, convex hull=24)
- After retessellation of defect 10, euler #=-14 (161210,483317,322093) : difference with theory (-13) = 1
- CORRECTING DEFECT 11 (vertices=8, convex hull=23)
- After retessellation of defect 11, euler #=-13 (161211,483327,322103) : difference with theory (-12) = 1
- CORRECTING DEFECT 12 (vertices=13, convex hull=38)
- After retessellation of defect 12, euler #=-12 (161216,483355,322127) : difference with theory (-11) = 1
- CORRECTING DEFECT 13 (vertices=31, convex hull=27)
- After retessellation of defect 13, euler #=-11 (161222,483382,322149) : difference with theory (-10) = 1
- CORRECTING DEFECT 14 (vertices=92, convex hull=92)
- After retessellation of defect 14, euler #=-10 (161258,483534,322266) : difference with theory (-9) = 1
- CORRECTING DEFECT 15 (vertices=28, convex hull=30)
- After retessellation of defect 15, euler #=-9 (161261,483553,322283) : difference with theory (-8) = 1
- CORRECTING DEFECT 16 (vertices=53, convex hull=41)
- After retessellation of defect 16, euler #=-7 (161270,483596,322319) : difference with theory (-7) = 0
- CORRECTING DEFECT 17 (vertices=59, convex hull=80)
- After retessellation of defect 17, euler #=-6 (161306,483739,322427) : difference with theory (-6) = 0
- CORRECTING DEFECT 18 (vertices=80, convex hull=50)
- After retessellation of defect 18, euler #=-5 (161324,483811,322482) : difference with theory (-5) = 0
- CORRECTING DEFECT 19 (vertices=115, convex hull=63)
- After retessellation of defect 19, euler #=-4 (161330,483858,322524) : difference with theory (-4) = 0
- CORRECTING DEFECT 20 (vertices=27, convex hull=19)
- After retessellation of defect 20, euler #=-3 (161336,483880,322541) : difference with theory (-3) = 0
- CORRECTING DEFECT 21 (vertices=22, convex hull=31)
- After retessellation of defect 21, euler #=-2 (161337,483893,322554) : difference with theory (-2) = 0
- CORRECTING DEFECT 22 (vertices=47, convex hull=43)
- After retessellation of defect 22, euler #=-1 (161346,483934,322587) : difference with theory (-1) = 0
- CORRECTING DEFECT 23 (vertices=24, convex hull=45)
- After retessellation of defect 23, euler #=0 (161359,483989,322630) : difference with theory (0) = 0
- CORRECTING DEFECT 24 (vertices=61, convex hull=90)
- After retessellation of defect 24, euler #=1 (161382,484095,322714) : difference with theory (1) = 0
- CORRECTING DEFECT 25 (vertices=78, convex hull=105)
- After retessellation of defect 25, euler #=2 (161415,484239,322826) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.08-->8.27) (max @ vno 34095 --> 40931)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.21 (0.08-->8.27) (max @ vno 34095 --> 40931)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 142 mutations (41.8%), 198 crossovers (58.2%), 99 vertices were eliminated
- building final representation...
- 1013 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=161415, nf=322826, ne=484239, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 20.3 minutes
- 0 defective edges
- removing intersecting faces
- 000: 160 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 161415 - 484239 + 322826 = 2 --> 0 holes
- F =2V-4: 322826 = 322830-4 (0)
- 2E=3F: 968478 = 968478 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 22 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 20:53:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub002 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/sub002/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- 19992 bright wm thresholded.
- 328 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.orig...
- computing class statistics...
- border white: 305608 voxels (1.82%)
- border gray 333888 voxels (1.99%)
- WM (92.0): 93.4 +- 9.8 [70.0 --> 110.0]
- GM (76.0) : 74.4 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.1 (was 70)
- setting MAX_BORDER_WHITE to 114.8 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.2 (was 40)
- setting MAX_GRAY to 95.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.3 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.01-->3.22) (max @ vno 88276 --> 88345)
- face area 0.28 +- 0.12 (0.00-->1.90)
- mean absolute distance = 0.72 +- 0.88
- 3895 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 92.8, mean outside = 69.2
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=73.1, 25 (25) missing vertices, mean dist 0.4 [0.6 (%30.0)->0.8 (%70.0))]
- %68 local maxima, %27 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 (0.11-->4.00) (max @ vno 109067 --> 107853)
- face area 0.28 +- 0.13 (0.00-->2.60)
- mean absolute distance = 0.35 +- 0.55
- 3538 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8317066.0, rms=13.35
- 001: dt: 0.5000, sse=8165330.5, rms=9.550 (0.000%)
- 002: dt: 0.5000, sse=8449409.0, rms=7.326 (0.000%)
- 003: dt: 0.5000, sse=8621062.0, rms=5.874 (0.000%)
- 004: dt: 0.5000, sse=8929902.0, rms=5.026 (0.000%)
- 005: dt: 0.5000, sse=9071069.0, rms=4.546 (0.000%)
- 006: dt: 0.5000, sse=9274709.0, rms=4.326 (0.000%)
- 007: dt: 0.5000, sse=9274201.0, rms=4.198 (0.000%)
- 008: dt: 0.5000, sse=9350852.0, rms=4.140 (0.000%)
- rms = 4.09, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=9256373.0, rms=4.091 (0.000%)
- 010: dt: 0.2500, sse=5720867.0, rms=2.771 (0.000%)
- 011: dt: 0.2500, sse=5169455.5, rms=2.321 (0.000%)
- 012: dt: 0.2500, sse=4855256.5, rms=2.202 (0.000%)
- 013: dt: 0.2500, sse=4759121.0, rms=2.112 (0.000%)
- rms = 2.07, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4662509.5, rms=2.068 (0.000%)
- 015: dt: 0.1250, sse=4467816.0, rms=1.889 (0.000%)
- rms = 1.87, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4421935.0, rms=1.867 (0.000%)
- positioning took 2.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=77.9, 44 (5) missing vertices, mean dist -0.2 [0.4 (%78.3)->0.2 (%21.7))]
- %79 local maxima, %16 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-->3.57) (max @ vno 95101 --> 88276)
- face area 0.35 +- 0.16 (0.00-->3.14)
- mean absolute distance = 0.23 +- 0.33
- 3311 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5680000.5, rms=6.27
- 017: dt: 0.5000, sse=5734551.0, rms=3.995 (0.000%)
- rms = 4.26, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5213045.5, rms=2.923 (0.000%)
- 019: dt: 0.2500, sse=4998928.0, rms=2.247 (0.000%)
- 020: dt: 0.2500, sse=4888233.5, rms=1.849 (0.000%)
- 021: dt: 0.2500, sse=4858575.0, rms=1.775 (0.000%)
- 022: dt: 0.2500, sse=4773433.0, rms=1.690 (0.000%)
- rms = 1.68, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4783839.5, rms=1.677 (0.000%)
- 024: dt: 0.1250, sse=4644433.0, rms=1.530 (0.000%)
- rms = 1.52, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4604391.5, rms=1.520 (0.000%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=81.3, 24 (2) missing vertices, mean dist -0.1 [0.2 (%76.7)->0.2 (%23.3))]
- %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.08-->3.73) (max @ vno 95101 --> 88276)
- face area 0.34 +- 0.16 (0.00-->3.37)
- mean absolute distance = 0.17 +- 0.26
- 3000 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5106248.5, rms=4.44
- 026: dt: 0.5000, sse=5414753.0, rms=3.830 (0.000%)
- rms = 4.09, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4915324.0, rms=2.426 (0.000%)
- 028: dt: 0.2500, sse=4796905.0, rms=1.914 (0.000%)
- 029: dt: 0.2500, sse=4821499.5, rms=1.594 (0.000%)
- rms = 1.62, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4760085.5, rms=1.489 (0.000%)
- 031: dt: 0.1250, sse=4681302.0, rms=1.345 (0.000%)
- rms = 1.33, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4645796.0, rms=1.335 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=82.4, 27 (1) missing vertices, mean dist -0.0 [0.2 (%58.2)->0.2 (%41.8))]
- %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4677926.5, rms=1.82
- rms = 2.60, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4779034.0, rms=1.175 (0.000%)
- 034: dt: 0.2500, sse=4958395.5, rms=1.004 (0.000%)
- rms = 1.01, time step reduction 2 of 3 to 0.125...
- rms = 1.00, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4959446.5, rms=0.995 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- generating cortex label...
- 13 non-cortical segments detected
- only using segment with 2118 vertices
- erasing segment 0 (vno[0] = 60122)
- erasing segment 2 (vno[0] = 70346)
- erasing segment 3 (vno[0] = 98641)
- erasing segment 4 (vno[0] = 102033)
- erasing segment 5 (vno[0] = 103304)
- erasing segment 6 (vno[0] = 105456)
- erasing segment 7 (vno[0] = 114353)
- erasing segment 8 (vno[0] = 116649)
- erasing segment 9 (vno[0] = 118813)
- erasing segment 10 (vno[0] = 118820)
- erasing segment 11 (vno[0] = 118832)
- erasing segment 12 (vno[0] = 122029)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.area
- vertex spacing 0.89 +- 0.25 (0.06-->3.75) (max @ vno 95101 --> 88276)
- face area 0.33 +- 0.16 (0.00-->3.44)
- refinement took 8.3 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 21:02:09 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 21:02:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 50.2 mm, total surface area = 98781 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.113 (target=0.015)
step 005: RMS=0.079 (target=0.015)
step 010: RMS=0.057 (target=0.015)
step 015: RMS=0.047 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.023 (target=0.015)
step 040: RMS=0.020 (target=0.015)
step 045: RMS=0.018 (target=0.015)
step 050: RMS=0.017 (target=0.015)
step 055: RMS=0.016 (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
- 214 vertices thresholded to be in k1 ~ [-0.26 0.52], k2 ~ [-0.25 0.07]
- total integrated curvature = 0.555*4pi (6.974) --> 0 handles
- ICI = 1.6, FI = 10.8, variation=181.540
- 187 vertices thresholded to be in [-0.06 0.01]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 133 vertices thresholded to be in [-0.14 0.14]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.022
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 21:05:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub002 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 [ sub002/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 [ 292 ]
- Gb_filter = 0
- WARN: S lookup min: -0.303609
- WARN: S explicit min: 0.000000 vertex = 322
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 21:05:09 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 0.272...
- 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 %21.39
- pass 1: epoch 2 of 3 starting distance error %21.26
- unfolding complete - removing small folds...
- starting distance error %21.16
- removing remaining folds...
- final distance error %21.18
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.28 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 22:21:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 0.606
- curvature mean = 0.027, std = 0.937
- curvature mean = 0.022, std = 0.843
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 429057.7, tmin=1.5316
- d=32.00 min @ (8.00, 8.00, 0.00) sse = 296682.4, tmin=2.8995
- d=8.00 min @ (-2.00, 0.00, 0.00) sse = 291731.8, tmin=5.6238
- d=4.00 min @ (0.00, 0.00, -1.00) sse = 289867.4, tmin=6.9905
- d=2.00 min @ (0.50, 0.00, 0.00) sse = 289076.8, tmin=8.3849
- d=0.50 min @ (0.00, -0.12, 0.12) sse = 289007.9, tmin=11.1425
- 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 11.14 min
- curvature mean = 0.015, std = 0.939
- curvature mean = 0.010, std = 0.928
- curvature mean = 0.012, std = 0.946
- curvature mean = 0.005, std = 0.965
- curvature mean = 0.011, std = 0.946
- curvature mean = 0.001, std = 0.983
- 2 Reading smoothwm
- curvature mean = -0.022, std = 0.386
- curvature mean = 0.006, std = 0.069
- curvature mean = 0.050, std = 0.237
- curvature mean = 0.007, std = 0.081
- curvature mean = 0.026, std = 0.375
- curvature mean = 0.007, std = 0.087
- curvature mean = 0.014, std = 0.482
- curvature mean = 0.007, std = 0.089
- curvature mean = 0.005, std = 0.568
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 22:58:34 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 22:58:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 22:58:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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...
- 1420 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3473 changed, 161415 examined...
- 001: 803 changed, 14502 examined...
- 002: 165 changed, 4497 examined...
- 003: 63 changed, 1016 examined...
- 004: 30 changed, 362 examined...
- 005: 12 changed, 194 examined...
- 006: 10 changed, 81 examined...
- 007: 6 changed, 49 examined...
- 008: 3 changed, 38 examined...
- 009: 1 changed, 20 examined...
- 010: 0 changed, 7 examined...
- 224 labels changed using aseg
- 000: 119 total segments, 79 labels (537 vertices) changed
- 001: 43 total segments, 3 labels (20 vertices) changed
- 002: 40 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 43 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 2286 vertices marked for relabeling...
- 2286 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 32 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 23:00:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub002 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/sub002/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- 19992 bright wm thresholded.
- 328 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.orig...
- computing class statistics...
- border white: 305608 voxels (1.82%)
- border gray 333888 voxels (1.99%)
- WM (92.0): 93.4 +- 9.8 [70.0 --> 110.0]
- GM (76.0) : 74.4 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.1 (was 70)
- setting MAX_BORDER_WHITE to 114.8 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.2 (was 40)
- setting MAX_GRAY to 95.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.3 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 92.8, mean outside = 69.2
- 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/sub002/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.01-->3.22) (max @ vno 88276 --> 88345)
- face area 0.28 +- 0.12 (0.00-->1.90)
- mean absolute distance = 0.72 +- 0.88
- 3975 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 25 points - only 0.00% unknown
- deleting segment 1 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 4 with 50 points - only 0.00% unknown
- deleting segment 5 with 496 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- mean border=73.1, 25 (25) missing vertices, mean dist 0.4 [0.6 (%30.0)->0.8 (%70.0))]
- %69 local maxima, %27 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 (0.11-->4.00) (max @ vno 109067 --> 107853)
- face area 0.28 +- 0.13 (0.00-->2.60)
- mean absolute distance = 0.35 +- 0.55
- 3587 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8333758.0, rms=13.34
- 001: dt: 0.5000, sse=8182196.0, rms=9.540 (0.000%)
- 002: dt: 0.5000, sse=8470299.0, rms=7.319 (0.000%)
- 003: dt: 0.5000, sse=8647821.0, rms=5.869 (0.000%)
- 004: dt: 0.5000, sse=8955117.0, rms=5.022 (0.000%)
- 005: dt: 0.5000, sse=9099352.0, rms=4.543 (0.000%)
- 006: dt: 0.5000, sse=9303448.0, rms=4.323 (0.000%)
- 007: dt: 0.5000, sse=9304492.0, rms=4.195 (0.000%)
- 008: dt: 0.5000, sse=9378339.0, rms=4.137 (0.000%)
- rms = 4.09, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=9287376.0, rms=4.088 (0.000%)
- 010: dt: 0.2500, sse=5736678.0, rms=2.770 (0.000%)
- 011: dt: 0.2500, sse=5185290.0, rms=2.320 (0.000%)
- 012: dt: 0.2500, sse=4869467.5, rms=2.202 (0.000%)
- 013: dt: 0.2500, sse=4773433.5, rms=2.112 (0.000%)
- rms = 2.07, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4677847.5, rms=2.068 (0.000%)
- 015: dt: 0.1250, sse=4482472.5, rms=1.889 (0.000%)
- rms = 1.87, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4436700.5, rms=1.867 (0.000%)
- positioning took 2.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 24 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 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 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 72 points - only 0.00% unknown
- deleting segment 7 with 283 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 15 with 24 points - only 29.17% unknown
- removing 4 vertex label from ripped group
- deleting segment 17 with 4 points - only 0.00% unknown
- deleting segment 18 with 16 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 19 with 4 points - only 0.00% unknown
- mean border=77.8, 44 (5) missing vertices, mean dist -0.2 [0.4 (%78.3)->0.2 (%21.7))]
- %80 local maxima, %16 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-->3.57) (max @ vno 95101 --> 88276)
- face area 0.35 +- 0.16 (0.00-->3.14)
- mean absolute distance = 0.23 +- 0.33
- 3358 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5699114.5, rms=6.27
- 017: dt: 0.5000, sse=5750167.5, rms=3.991 (0.000%)
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5230811.5, rms=2.920 (0.000%)
- 019: dt: 0.2500, sse=5019653.5, rms=2.246 (0.000%)
- 020: dt: 0.2500, sse=4913185.0, rms=1.850 (0.000%)
- 021: dt: 0.2500, sse=4876328.0, rms=1.775 (0.000%)
- 022: dt: 0.2500, sse=4794801.5, rms=1.691 (0.000%)
- rms = 1.68, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4804935.0, rms=1.678 (0.000%)
- 024: dt: 0.1250, sse=4666340.5, rms=1.532 (0.000%)
- rms = 1.52, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4626848.5, rms=1.521 (0.000%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 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 66 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- deleting segment 7 with 357 points - only 0.00% unknown
- removing 4 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
- deleting segment 13 with 24 points - only 29.17% unknown
- deleting segment 14 with 14 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 15 with 4 points - only 0.00% unknown
- mean border=81.3, 34 (2) missing vertices, mean dist -0.1 [0.2 (%76.7)->0.2 (%23.3))]
- %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.24 (0.07-->3.73) (max @ vno 95101 --> 88276)
- face area 0.34 +- 0.16 (0.00-->3.37)
- mean absolute distance = 0.17 +- 0.26
- 3098 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5132227.0, rms=4.43
- 026: dt: 0.5000, sse=5441496.5, rms=3.825 (0.000%)
- rms = 4.09, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4940717.5, rms=2.424 (0.000%)
- 028: dt: 0.2500, sse=4822029.0, rms=1.914 (0.000%)
- 029: dt: 0.2500, sse=4847129.0, rms=1.595 (0.000%)
- rms = 1.62, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4785154.0, rms=1.491 (0.000%)
- 031: dt: 0.1250, sse=4705179.0, rms=1.347 (0.000%)
- rms = 1.34, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4669167.5, rms=1.337 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- deleting segment 3 with 75 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 369 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 30 points - only 43.33% unknown
- deleting segment 10 with 16 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 11 with 4 points - only 0.00% unknown
- mean border=82.3, 32 (1) missing vertices, mean dist -0.0 [0.2 (%58.2)->0.2 (%41.8))]
- %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4702632.0, rms=1.82
- rms = 2.60, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4805202.0, rms=1.179 (0.000%)
- 034: dt: 0.2500, sse=4988136.5, rms=1.006 (0.000%)
- rms = 1.01, time step reduction 2 of 3 to 0.125...
- rms = 1.00, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4988835.0, rms=0.998 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- smoothing surface for 5 iterations...
- mean border=50.1, 21 (21) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.3 (%100.0))]
- %17 local maxima, %60 large gradients and %18 min vals, 1494 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=34150712.0, rms=31.67
- 001: dt: 0.5000, sse=24474122.0, rms=26.267 (0.000%)
- 002: dt: 0.5000, sse=17722590.0, rms=21.738 (0.000%)
- 003: dt: 0.5000, sse=13278174.0, rms=18.063 (0.000%)
- 004: dt: 0.5000, sse=10660978.0, rms=15.162 (0.000%)
- 005: dt: 0.5000, sse=9172553.0, rms=12.923 (0.000%)
- 006: dt: 0.5000, sse=8388446.5, rms=11.195 (0.000%)
- 007: dt: 0.5000, sse=7906671.0, rms=9.716 (0.000%)
- 008: dt: 0.5000, sse=7596661.0, rms=8.370 (0.000%)
- 009: dt: 0.5000, sse=7479242.0, rms=7.144 (0.000%)
- 010: dt: 0.5000, sse=7444399.0, rms=6.139 (0.000%)
- 011: dt: 0.5000, sse=7613262.0, rms=5.370 (0.000%)
- 012: dt: 0.5000, sse=7775754.0, rms=4.854 (0.000%)
- 013: dt: 0.5000, sse=7940431.5, rms=4.521 (0.000%)
- 014: dt: 0.5000, sse=8061841.0, rms=4.339 (0.000%)
- 015: dt: 0.5000, sse=8165478.0, rms=4.189 (0.000%)
- 016: dt: 0.5000, sse=8227836.0, rms=4.111 (0.000%)
- 017: dt: 0.5000, sse=8254363.0, rms=4.038 (0.000%)
- rms = 4.01, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=8280509.0, rms=4.006 (0.000%)
- 019: dt: 0.2500, sse=5527110.0, rms=3.130 (0.000%)
- 020: dt: 0.2500, sse=5281470.5, rms=2.884 (0.000%)
- rms = 2.84, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=5098633.5, rms=2.843 (0.000%)
- 022: dt: 0.1250, sse=4846981.5, rms=2.690 (0.000%)
- rms = 2.67, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4809324.0, rms=2.670 (0.000%)
- positioning took 3.2 minutes
- mean border=47.2, 724 (2) missing vertices, mean dist 0.2 [0.2 (%43.5)->0.5 (%56.5))]
- %40 local maxima, %42 large gradients and %14 min vals, 390 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=5689631.0, rms=5.24
- 024: dt: 0.5000, sse=5874995.0, rms=4.165 (0.000%)
- rms = 4.17, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=5432156.0, rms=3.457 (0.000%)
- 026: dt: 0.2500, sse=5495592.5, rms=3.086 (0.000%)
- 027: dt: 0.2500, sse=5408624.0, rms=2.927 (0.000%)
- 028: dt: 0.2500, sse=5454962.0, rms=2.838 (0.000%)
- 029: dt: 0.2500, sse=5432246.5, rms=2.783 (0.000%)
- rms = 2.75, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=5497902.0, rms=2.746 (0.000%)
- 031: dt: 0.1250, sse=5270643.0, rms=2.579 (0.000%)
- rms = 2.55, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=5244988.5, rms=2.550 (0.000%)
- positioning took 1.3 minutes
- mean border=44.4, 909 (1) missing vertices, mean dist 0.2 [0.2 (%33.6)->0.4 (%66.4))]
- %61 local maxima, %21 large gradients and %13 min vals, 473 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=5684017.0, rms=4.45
- 033: dt: 0.5000, sse=5879174.0, rms=4.061 (0.000%)
- rms = 4.14, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=5464883.0, rms=3.090 (0.000%)
- 035: dt: 0.2500, sse=5690023.0, rms=2.708 (0.000%)
- 036: dt: 0.2500, sse=5633554.0, rms=2.621 (0.000%)
- rms = 2.59, time step reduction 2 of 3 to 0.125...
- 037: dt: 0.2500, sse=5691973.0, rms=2.592 (0.000%)
- 038: dt: 0.1250, sse=5451668.5, rms=2.400 (0.000%)
- rms = 2.37, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=5432180.0, rms=2.373 (0.000%)
- positioning took 1.1 minutes
- mean border=43.1, 1810 (1) missing vertices, mean dist 0.1 [0.2 (%43.0)->0.3 (%57.0))]
- %65 local maxima, %16 large gradients and %13 min vals, 386 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/sub002/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=5503922.5, rms=2.83
- rms = 3.78, time step reduction 1 of 3 to 0.250...
- 040: dt: 0.2500, sse=5343033.5, rms=2.470 (0.000%)
- 041: dt: 0.2500, sse=5533832.0, rms=2.390 (0.000%)
- rms = 2.37, time step reduction 2 of 3 to 0.125...
- 042: dt: 0.2500, sse=5608822.5, rms=2.372 (0.000%)
- 043: dt: 0.1250, sse=5512340.5, rms=2.247 (0.000%)
- rms = 2.23, time step reduction 3 of 3 to 0.062...
- 044: dt: 0.1250, sse=5511996.5, rms=2.234 (0.000%)
- positioning took 0.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.area.pial
- vertex spacing 1.00 +- 0.41 (0.08-->6.08) (max @ vno 112370 --> 113418)
- face area 0.40 +- 0.29 (0.00-->6.39)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 161415 vertices processed
- 25000 of 161415 vertices processed
- 50000 of 161415 vertices processed
- 75000 of 161415 vertices processed
- 100000 of 161415 vertices processed
- 125000 of 161415 vertices processed
- 150000 of 161415 vertices processed
- 0 of 161415 vertices processed
- 25000 of 161415 vertices processed
- 50000 of 161415 vertices processed
- 75000 of 161415 vertices processed
- 100000 of 161415 vertices processed
- 125000 of 161415 vertices processed
- 150000 of 161415 vertices processed
- thickness calculation complete, 365:767 truncations.
- 39775 vertices at 0 distance
- 116248 vertices at 1 distance
- 101662 vertices at 2 distance
- 37656 vertices at 3 distance
- 10030 vertices at 4 distance
- 2812 vertices at 5 distance
- 905 vertices at 6 distance
- 308 vertices at 7 distance
- 136 vertices at 8 distance
- 75 vertices at 9 distance
- 35 vertices at 10 distance
- 26 vertices at 11 distance
- 23 vertices at 12 distance
- 14 vertices at 13 distance
- 13 vertices at 14 distance
- 6 vertices at 15 distance
- 11 vertices at 16 distance
- 10 vertices at 17 distance
- 22 vertices at 18 distance
- 11 vertices at 19 distance
- 6 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.thickness
- positioning took 16.5 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 23:16:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 23:16:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- pctsurfcon --s sub002 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/pctsurfcon.log
- Thu Aug 8 23:16:45 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.wm.mgh --regheader sub002 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 125441
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.wm.mgh
- Dim: 161415 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.gm.mgh --projfrac 0.3 --regheader sub002 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 143811
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.gm.mgh
- Dim: 161415 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.w-g.pct.mgh --annot sub002 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.w-g.pct.mgh --annot sub002 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.w-g.pct.mgh
- Vertex Area is 0.665893 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1613 1104.939
- 2 2002 caudalanteriorcingulate 1478 1023.718
- 3 2003 caudalmiddlefrontal 3479 2355.313
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2789 1858.148
- 6 2006 entorhinal 420 283.363
- 7 2007 fusiform 5769 3930.761
- 8 2008 inferiorparietal 11200 7539.997
- 9 2009 inferiortemporal 5803 3916.349
- 10 2010 isthmuscingulate 2105 1342.184
- 11 2011 lateraloccipital 7148 4593.353
- 12 2012 lateralorbitofrontal 4055 2705.177
- 13 2013 lingual 5270 3473.353
- 14 2014 medialorbitofrontal 2784 1895.848
- 15 2015 middletemporal 5977 4047.395
- 16 2016 parahippocampal 1128 776.200
- 17 2017 paracentral 2662 1693.575
- 18 2018 parsopercularis 3045 2090.832
- 19 2019 parsorbitalis 1263 882.700
- 20 2020 parstriangularis 2760 1867.343
- 21 2021 pericalcarine 2321 1586.182
- 22 2022 postcentral 7468 4850.527
- 23 2023 posteriorcingulate 1766 1200.175
- 24 2024 precentral 7961 5063.128
- 25 2025 precuneus 8644 5767.969
- 26 2026 rostralanteriorcingulate 1579 1029.918
- 27 2027 rostralmiddlefrontal 11351 7817.396
- 28 2028 superiorfrontal 12638 8630.331
- 29 2029 superiorparietal 10332 6731.142
- 30 2030 superiortemporal 5877 3950.300
- 31 2031 supramarginal 6365 4261.914
- 32 2032 frontalpole 435 309.395
- 33 2033 temporalpole 673 460.947
- 34 2034 transversetemporal 641 381.213
- 35 2035 insula 3677 2431.106
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 23:17:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 1613 1105 2837 2.642 0.377 0.113 0.034 16 2.4 bankssts
- 1478 1024 2713 2.681 0.711 0.142 0.040 23 2.4 caudalanteriorcingulate
- 3479 2355 6316 2.418 0.444 0.129 0.045 42 6.1 caudalmiddlefrontal
- 2789 1858 4005 1.969 0.447 0.172 0.070 123 8.4 cuneus
- 420 283 1663 3.568 0.920 0.168 0.101 8 1.7 entorhinal
- 5769 3931 11718 2.625 0.605 0.139 0.049 94 11.3 fusiform
- 11200 7540 20133 2.428 0.459 0.146 0.049 193 22.4 inferiorparietal
- 5803 3916 12570 2.605 0.639 0.150 0.062 113 15.0 inferiortemporal
- 2105 1342 3132 2.133 0.889 0.146 0.061 36 4.9 isthmuscingulate
- 7148 4593 11257 2.210 0.414 0.152 0.057 132 15.7 lateraloccipital
- 4055 2705 7839 2.595 0.638 0.153 0.066 75 9.9 lateralorbitofrontal
- 5270 3473 8584 2.284 0.600 0.165 0.070 105 14.7 lingual
- 2784 1896 4873 2.237 0.714 0.153 0.137 65 7.6 medialorbitofrontal
- 5977 4047 13994 2.859 0.636 0.146 0.054 106 12.7 middletemporal
- 1128 776 2141 2.463 0.531 0.124 0.041 11 1.9 parahippocampal
- 2662 1694 4605 2.469 0.619 0.127 0.045 50 4.6 paracentral
- 3045 2091 5779 2.492 0.450 0.124 0.035 35 4.6 parsopercularis
- 1263 883 2644 2.344 0.610 0.139 0.040 17 2.0 parsorbitalis
- 2760 1867 4788 2.265 0.564 0.137 0.043 38 5.0 parstriangularis
- 2321 1586 2791 1.850 0.436 0.141 0.096 33 4.9 pericalcarine
- 7468 4851 11036 2.030 0.599 0.133 0.047 139 16.0 postcentral
- 1766 1200 3117 2.381 0.834 0.140 0.049 27 3.4 posteriorcingulate
- 7961 5063 13852 2.520 0.544 0.119 0.042 81 14.4 precentral
- 8644 5768 14928 2.458 0.501 0.135 0.047 120 17.3 precuneus
- 1579 1030 3130 2.682 0.603 0.132 0.051 26 3.4 rostralanteriorcingulate
- 11351 7817 19933 2.266 0.499 0.149 0.057 202 24.2 rostralmiddlefrontal
- 12638 8630 25666 2.622 0.572 0.151 0.066 265 33.0 superiorfrontal
- 10332 6731 16404 2.182 0.403 0.140 1.071 195 20.5 superiorparietal
- 5877 3950 13009 2.944 0.583 0.126 0.043 76 10.9 superiortemporal
- 6365 4262 11327 2.403 0.485 0.128 0.041 114 11.0 supramarginal
- 435 309 1051 2.470 0.543 0.207 0.110 16 1.6 frontalpole
- 673 461 2425 3.689 0.857 0.163 0.068 12 1.9 temporalpole
- 641 381 1154 2.538 0.344 0.130 0.045 9 1.2 transversetemporal
- 3677 2431 7937 3.061 0.862 0.135 0.090 110 10.9 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 23:17:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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...
- 12 labels changed using aseg
- relabeling using gibbs priors...
- 000: 11329 changed, 161415 examined...
- 001: 2697 changed, 43014 examined...
- 002: 834 changed, 13857 examined...
- 003: 368 changed, 4630 examined...
- 004: 174 changed, 1978 examined...
- 005: 100 changed, 1002 examined...
- 006: 53 changed, 581 examined...
- 007: 34 changed, 276 examined...
- 008: 20 changed, 186 examined...
- 009: 17 changed, 118 examined...
- 010: 8 changed, 86 examined...
- 011: 3 changed, 40 examined...
- 012: 2 changed, 20 examined...
- 013: 0 changed, 14 examined...
- 5 labels changed using aseg
- 000: 338 total segments, 250 labels (3247 vertices) changed
- 001: 110 total segments, 24 labels (259 vertices) changed
- 002: 86 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 175 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1494 vertices marked for relabeling...
- 1494 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 24 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 23:18:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 1175 819 2113 2.369 0.600 0.180 0.070 31 3.5 G_and_S_frontomargin
- 1303 854 2009 2.203 0.431 0.143 0.048 18 2.6 G_and_S_occipital_inf
- 1671 971 2616 2.244 0.641 0.131 0.052 40 3.2 G_and_S_paracentral
- 1573 1059 3193 2.634 0.531 0.155 0.049 26 3.2 G_and_S_subcentral
- 1500 1018 3301 2.518 0.478 0.182 0.076 41 4.4 G_and_S_transv_frontopol
- 3269 2207 5869 2.518 0.552 0.139 0.047 46 6.6 G_and_S_cingul-Ant
- 2054 1450 3907 2.609 0.444 0.121 0.030 20 2.6 G_and_S_cingul-Mid-Ant
- 1832 1290 3447 2.542 0.547 0.128 0.035 20 2.5 G_and_S_cingul-Mid-Post
- 651 405 1530 2.881 0.799 0.172 0.072 15 1.9 G_cingul-Post-dorsal
- 340 225 675 2.537 0.810 0.183 0.082 8 1.1 G_cingul-Post-ventral
- 2499 1715 3611 1.903 0.495 0.185 0.073 57 7.2 G_cuneus
- 1637 1121 3759 2.757 0.408 0.144 0.054 30 3.6 G_front_inf-Opercular
- 439 295 1007 2.585 0.426 0.130 0.042 7 0.7 G_front_inf-Orbital
- 1557 1049 3164 2.389 0.572 0.151 0.051 29 3.4 G_front_inf-Triangul
- 5032 3428 10616 2.448 0.470 0.161 0.078 113 13.4 G_front_middle
- 8077 5478 18872 2.751 0.587 0.171 0.085 209 27.7 G_front_sup
- 570 369 1513 3.518 0.572 0.131 0.061 14 1.2 G_Ins_lg_and_S_cent_ins
- 735 486 2585 3.926 0.752 0.149 0.090 20 2.3 G_insular_short
- 2843 1846 5463 2.393 0.423 0.159 0.056 64 6.3 G_occipital_middle
- 2442 1545 4035 2.173 0.402 0.142 0.043 36 4.1 G_occipital_sup
- 2586 1695 6493 2.906 0.587 0.155 0.056 61 6.0 G_oc-temp_lat-fusifor
- 3373 2234 5578 2.218 0.617 0.176 0.080 76 10.6 G_oc-temp_med-Lingual
- 1422 905 3494 2.882 0.871 0.160 0.148 75 6.9 G_oc-temp_med-Parahip
- 2933 2003 6824 2.595 0.623 0.167 0.063 63 7.7 G_orbital
- 4612 3049 9907 2.576 0.512 0.167 0.063 106 11.9 G_pariet_inf-Angular
- 3278 2193 6827 2.548 0.466 0.139 0.047 55 6.1 G_pariet_inf-Supramar
- 2870 1884 5371 2.291 0.386 0.145 0.053 52 6.1 G_parietal_sup
- 2734 1709 4491 2.089 0.496 0.140 0.061 85 8.5 G_postcentral
- 3208 1892 6767 2.780 0.443 0.122 0.054 43 7.5 G_precentral
- 3549 2321 7434 2.543 0.442 0.146 3.042 110 9.8 G_precuneus
- 730 489 1594 2.367 0.607 0.208 0.391 39 3.8 G_rectus
- 443 300 880 2.599 1.056 0.079 0.028 2 0.4 G_subcallosal
- 525 305 1054 2.634 0.352 0.130 0.050 8 1.0 G_temp_sup-G_T_transv
- 1829 1212 5204 3.148 0.526 0.155 0.071 44 5.5 G_temp_sup-Lateral
- 828 599 2485 3.619 0.610 0.132 0.045 9 1.7 G_temp_sup-Plan_polar
- 975 652 1915 2.561 0.416 0.123 0.033 11 1.3 G_temp_sup-Plan_tempo
- 3383 2256 8692 2.807 0.620 0.166 0.079 86 10.9 G_temporal_inf
- 3388 2310 9423 3.044 0.627 0.160 0.063 77 8.2 G_temporal_middle
- 463 300 541 1.937 0.409 0.091 0.022 2 0.4 Lat_Fis-ant-Horizont
- 218 148 352 2.722 0.512 0.119 0.030 2 0.3 Lat_Fis-ant-Vertical
- 1684 1138 2330 2.400 0.444 0.113 0.033 10 2.3 Lat_Fis-post
- 3111 1968 4769 2.055 0.422 0.161 0.107 138 9.1 Pole_occipital
- 2121 1477 5973 2.827 0.928 0.179 0.091 53 7.3 Pole_temporal
- 2681 1771 3575 2.240 0.625 0.134 0.047 30 5.3 S_calcarine
- 3309 2224 3681 1.835 0.545 0.113 0.030 21 4.3 S_central
- 1403 981 2097 2.287 0.526 0.126 0.042 14 2.6 S_cingul-Marginalis
- 464 309 791 2.883 0.424 0.131 0.050 5 0.8 S_circular_insula_ant
- 1251 822 2013 2.869 0.591 0.091 0.022 5 1.2 S_circular_insula_inf
- 1585 1072 2242 2.318 0.468 0.103 0.030 9 1.9 S_circular_insula_sup
- 1027 686 1754 2.339 0.623 0.133 0.046 15 2.1 S_collat_transv_ant
- 522 355 716 2.181 0.364 0.148 0.044 6 1.1 S_collat_transv_post
- 2738 1898 4133 2.165 0.433 0.134 0.038 34 4.3 S_front_inf
- 2974 2053 4175 2.077 0.380 0.119 0.031 25 3.9 S_front_middle
- 2856 1964 4211 2.240 0.467 0.125 0.050 53 4.3 S_front_sup
- 694 474 825 2.078 0.383 0.120 0.055 38 1.9 S_interm_prim-Jensen
- 4156 2756 5500 2.104 0.388 0.123 0.034 42 5.6 S_intrapariet_and_P_trans
- 869 581 1405 2.444 0.546 0.163 0.053 16 1.8 S_oc_middle_and_Lunatus
- 1817 1246 2507 2.158 0.345 0.139 0.040 24 2.8 S_oc_sup_and_transversal
- 988 652 1642 2.371 0.359 0.122 0.038 11 1.5 S_occipital_ant
- 1431 974 2019 2.359 0.445 0.110 0.026 9 1.6 S_oc-temp_lat
- 2639 1855 4289 2.459 0.438 0.121 0.034 23 3.8 S_oc-temp_med_and_Lingual
- 527 367 655 1.922 0.408 0.134 0.037 4 0.8 S_orbital_lateral
- 818 565 1231 2.215 0.868 0.118 0.072 11 1.2 S_orbital_med-olfact
- 1538 1033 2484 2.450 0.603 0.138 0.046 20 3.0 S_orbital-H_Shaped
- 3307 2166 4512 2.333 0.505 0.119 0.041 30 6.1 S_parieto_occipital
- 2476 1568 2701 2.031 0.925 0.133 0.049 36 4.7 S_pericallosal
- 2963 1940 3597 1.981 0.404 0.122 0.035 30 4.1 S_postcentral
- 2262 1522 3647 2.399 0.412 0.102 0.024 14 2.4 S_precentral-inf-part
- 1494 1029 1883 2.137 0.482 0.115 0.029 10 1.9 S_precentral-sup-part
- 387 255 539 2.129 0.800 0.155 0.055 6 0.9 S_suborbital
- 2326 1578 3948 2.502 0.512 0.143 0.047 34 4.4 S_subparietal
- 1578 1078 2322 2.305 0.431 0.116 0.028 10 2.0 S_temporal_inf
- 7597 5171 12127 2.558 0.459 0.117 0.033 70 11.0 S_temporal_sup
- 337 241 445 2.147 0.324 0.135 0.033 3 0.5 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 23:19:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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...
- 959 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3377 changed, 161415 examined...
- 001: 813 changed, 13870 examined...
- 002: 193 changed, 4425 examined...
- 003: 79 changed, 1190 examined...
- 004: 46 changed, 488 examined...
- 005: 14 changed, 255 examined...
- 006: 6 changed, 100 examined...
- 007: 4 changed, 33 examined...
- 008: 1 changed, 27 examined...
- 009: 1 changed, 7 examined...
- 010: 0 changed, 7 examined...
- 127 labels changed using aseg
- 000: 67 total segments, 34 labels (207 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 64 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1322 vertices marked for relabeling...
- 1322 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 12 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 23:20:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 1653 1136 3208 2.721 0.700 0.144 0.043 27 3.0 caudalanteriorcingulate
- 3564 2412 6401 2.424 0.451 0.130 0.045 43 6.3 caudalmiddlefrontal
- 3659 2437 5248 2.010 0.425 0.161 0.061 132 9.7 cuneus
- 476 327 1682 3.355 1.035 0.162 0.084 8 1.8 entorhinal
- 5037 3419 10347 2.680 0.599 0.133 0.041 76 8.8 fusiform
- 10801 7240 18990 2.401 0.462 0.146 0.049 186 21.6 inferiorparietal
- 6489 4391 13948 2.581 0.636 0.153 0.066 129 17.3 inferiortemporal
- 2152 1376 3205 2.139 0.885 0.147 0.061 37 5.1 isthmuscingulate
- 7476 4807 11817 2.211 0.416 0.151 0.057 137 16.2 lateraloccipital
- 4594 3083 8972 2.556 0.667 0.160 0.078 106 13.1 lateralorbitofrontal
- 5308 3494 8646 2.284 0.597 0.165 0.070 105 14.7 lingual
- 2153 1465 4008 2.243 0.759 0.161 0.168 61 6.8 medialorbitofrontal
- 7282 4941 16404 2.822 0.605 0.141 0.050 120 14.7 middletemporal
- 1110 762 2098 2.466 0.528 0.123 0.041 11 1.9 parahippocampal
- 2821 1795 4951 2.486 0.610 0.128 0.045 52 4.8 paracentral
- 3044 2087 5729 2.496 0.450 0.122 0.035 34 4.5 parsopercularis
- 1352 925 2795 2.462 0.521 0.133 0.042 19 2.3 parsorbitalis
- 3108 2100 5525 2.275 0.557 0.146 0.048 51 6.0 parstriangularis
- 2310 1575 2782 1.855 0.439 0.142 0.097 34 4.9 pericalcarine
- 7976 5197 11894 2.036 0.587 0.135 0.047 149 17.1 postcentral
- 1818 1234 3169 2.382 0.822 0.139 0.049 27 3.4 posteriorcingulate
- 7665 4846 13434 2.521 0.545 0.118 0.042 78 14.0 precentral
- 8549 5706 14992 2.461 0.503 0.137 0.048 122 17.4 precuneus
- 1645 1084 3253 2.755 0.514 0.138 0.051 28 3.6 rostralanteriorcingulate
- 7543 5212 12893 2.217 0.476 0.145 0.057 125 15.7 rostralmiddlefrontal
- 16428 11254 32323 2.536 0.582 0.150 0.063 328 40.6 superiorfrontal
- 8695 5673 13901 2.186 0.411 0.139 1.264 172 17.5 superiorparietal
- 8094 5431 18356 2.975 0.641 0.134 0.054 150 18.0 superiortemporal
- 5799 3898 10121 2.389 0.473 0.126 0.041 104 10.0 supramarginal
- 617 368 1106 2.536 0.347 0.130 0.046 8 1.2 transversetemporal
- 3258 2177 7151 3.065 0.861 0.124 0.059 50 6.1 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 23:21:01 CEST 2013
- bbregister --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat.log
- Thu Aug 8 23:21:02 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999032, 0.0218052, 0.0381938)
- j_ras = (0.0265301, 0.991428, 0.127932)
- k_ras = (0.0350768, -0.128822, 0.991047)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii...
- fslregister --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fslregister.log
- Thu Aug 8 23:21:08 CEST 2013
- --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.19095e-09, 0)
- j_ras = (0, 1.49012e-08, -1)
- k_ras = (0, 1, 0)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/transforms/tmp.bbregister.19392/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999032, 0.0218052, 0.0381938)
- j_ras = (0.0265301, 0.991428, 0.127932)
- k_ras = (0.0350768, -0.128822, 0.991047)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311049
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/reg0.19435.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fsl.mat0 --s sub002 --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/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/reg0.19435.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/sub002/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/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.881;
- 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 -0.022 -0.038 0.000;
- 0.035 -0.129 0.991 -0.000;
- -0.027 -0.991 -0.128 0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 -0.022 -0.038 0.000;
- 0.035 -0.129 0.991 -0.000;
- -0.027 -0.991 -0.128 0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 0.999999
- subject = sub002
- RegMat ---------------------------
- 0.999 -0.022 -0.038 0.000;
- 0.035 -0.129 0.991 -0.000;
- -0.027 -0.991 -0.128 0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311049, ref det = -1
- Thu Aug 8 23:21:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/transforms/tmp.bbregister.19392/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fsl.mat0
- Thu Aug 8 23:25:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.999 -0.028 -0.022 38.022;
- -0.025 -0.094 -0.995 271.186;
- 0.025 0.995 -0.095 8.808;
- 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/sub002/mri/transforms/tmp.bbregister.19392/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/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/sub002/mri/transforms/tmp.bbregister.19392/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.881;
- 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 = -0.311049, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.999 -0.025 -0.025 -0.620;
- 0.022 -0.095 0.995 1.194;
- -0.028 -0.995 -0.094 -1.620;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 -0.025 -0.025 -0.620;
- 0.022 -0.095 0.995 1.194;
- -0.028 -0.995 -0.094 -1.620;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub002
- RegMat ---------------------------
- 0.999 -0.025 -0.025 -0.620;
- 0.022 -0.095 0.995 1.194;
- -0.028 -0.995 -0.094 -1.620;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 23:21:08 CEST 2013
- Ended at Thu Aug 8 23:31:41 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/transforms/tmp.bbregister.19392/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat
- subject sub002
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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 1376450912
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 -0.025 -0.025 -0.620;
- 0.022 -0.095 0.995 1.194;
- -0.028 -0.995 -0.094 -1.620;
- 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 1.045212
- 1 -25.0 -25.0 25.0 1.003322
- 2 -25.0 25.0 -25.0 1.007902
- 3 -25.0 25.0 25.0 1.026935
- 4 25.0 -25.0 -25.0 1.013771
- 5 25.0 -25.0 25.0 1.061154
- 6 25.0 25.0 -25.0 1.023364
- 7 25.0 25.0 25.0 1.010720
- REL: 8 0.315800 8.192379 1.024047 rel = 0.308384
- Initial costs ----------------
- Number of surface hits 3047
- WM Intensity 57.8110 +/- 8.6409
- Ctx Intensity 70.0825 +/- 11.1034
- Pct Contrast 18.8163 +/- 18.7598
- Cost 0.3158
- RelCost 0.3084
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9581 0.9581 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8927 0.8927 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8505 0.8505 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8266 0.8266 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7720 0.7720 0.0
- 301 0.0000 -4.0000 4.0000 -4.0000 0.0000 0.0000 0.7307 0.7307 0.0
- 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.7154 0.7154 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3158 0.3158 0.0
- Brute Force --------------------------
- Min cost was 0.315800
- Number of iterations 729
- Search time 2.638000 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 -0.038 0.000 0.000 0.000 0.000 0.000 0.3141953586
- 9 -0.089 0.000 0.000 0.000 0.000 0.000 0.3140502370
- 10 -0.067 0.000 0.000 0.000 0.000 0.000 0.3137921398
- 11 -0.066 0.000 0.000 0.000 0.000 0.000 0.3137911513
- 17 -0.066 -0.618 0.000 0.000 0.000 0.000 0.2756750169
- 19 -0.066 -0.587 0.000 0.000 0.000 0.000 0.2751719787
- 22 -0.066 -0.583 0.000 0.000 0.000 0.000 0.2751619203
- 26 -0.066 -0.583 1.000 0.000 0.000 0.000 0.1754425269
- 31 -0.066 -0.583 1.102 0.000 0.000 0.000 0.1711928032
- 33 -0.066 -0.583 1.196 0.000 0.000 0.000 0.1698448987
- 34 -0.066 -0.583 1.197 0.000 0.000 0.000 0.1698422257
- 35 -0.066 -0.583 1.207 0.000 0.000 0.000 0.1698337980
- 37 -0.066 -0.583 1.204 0.000 0.000 0.000 0.1698317278
- 38 -0.066 -0.583 1.203 0.000 0.000 0.000 0.1698315153
- 39 -0.066 -0.583 1.202 0.000 0.000 0.000 0.1698312767
- 41 -0.066 -0.583 1.201 0.000 0.000 0.000 0.1698309996
- 48 -0.066 -0.583 1.201 -0.143 0.000 0.000 0.1646940319
- 50 -0.066 -0.583 1.201 -0.125 0.000 0.000 0.1644750936
- 53 -0.066 -0.583 1.201 -0.112 0.000 0.000 0.1644734824
- 54 -0.066 -0.583 1.201 -0.118 0.000 0.000 0.1644524372
- 55 -0.066 -0.583 1.201 -0.119 0.000 0.000 0.1644516281
- 63 -0.066 -0.583 1.201 -0.119 -0.087 0.000 0.1642141626
- 67 -0.066 -0.583 1.201 -0.119 -0.116 0.000 0.1640114329
- 69 -0.066 -0.583 1.201 -0.119 -0.111 0.000 0.1639960182
- 77 -0.066 -0.583 1.201 -0.119 -0.111 0.382 0.1597704919
- 82 -0.066 -0.583 1.201 -0.119 -0.111 0.387 0.1597694456
- 83 -0.066 -0.583 1.201 -0.119 -0.111 0.385 0.1597666659
- 92 0.316 -0.583 1.201 -0.119 -0.111 0.385 0.1479585072
- 93 0.282 -0.583 1.201 -0.119 -0.111 0.385 0.1479536807
- 97 0.263 -0.583 1.201 -0.119 -0.111 0.385 0.1479532345
- 98 0.268 -0.583 1.201 -0.119 -0.111 0.385 0.1479499926
- 99 0.273 -0.583 1.201 -0.119 -0.111 0.385 0.1479497019
- 100 0.271 -0.583 1.201 -0.119 -0.111 0.385 0.1479482908
- 108 0.271 -0.651 1.201 -0.119 -0.111 0.385 0.1472668685
- 109 0.271 -0.655 1.201 -0.119 -0.111 0.385 0.1472428043
- 111 0.271 -0.692 1.201 -0.119 -0.111 0.385 0.1470721936
- 114 0.271 -0.690 1.201 -0.119 -0.111 0.385 0.1470695059
- 116 0.271 -0.689 1.201 -0.119 -0.111 0.385 0.1470688066
- 124 0.271 -0.689 1.205 -0.119 -0.111 0.385 0.1470313978
- 125 0.271 -0.689 1.242 -0.119 -0.111 0.385 0.1467459901
- 128 0.271 -0.689 1.236 -0.119 -0.111 0.385 0.1467363085
- 137 0.271 -0.689 1.236 -0.135 -0.111 0.385 0.1464510371
- 138 0.271 -0.689 1.236 -0.181 -0.111 0.385 0.1462013748
- 140 0.271 -0.689 1.236 -0.171 -0.111 0.385 0.1461816849
- 141 0.271 -0.689 1.236 -0.172 -0.111 0.385 0.1461805886
- 153 0.271 -0.689 1.236 -0.172 -0.115 0.385 0.1461751148
- 154 0.271 -0.689 1.236 -0.172 -0.116 0.385 0.1461750893
- 162 0.271 -0.689 1.236 -0.172 -0.116 0.481 0.1452244900
- 163 0.271 -0.689 1.236 -0.172 -0.116 0.475 0.1452053737
- 165 0.271 -0.689 1.236 -0.172 -0.116 0.474 0.1452050146
- 174 0.321 -0.689 1.236 -0.172 -0.116 0.474 0.1443831908
- 175 0.350 -0.689 1.236 -0.172 -0.116 0.474 0.1440496667
- 179 0.356 -0.689 1.236 -0.172 -0.116 0.474 0.1440469570
- 180 0.354 -0.689 1.236 -0.172 -0.116 0.474 0.1440446627
- 181 0.353 -0.689 1.236 -0.172 -0.116 0.474 0.1440445955
- 189 0.353 -0.657 1.236 -0.172 -0.116 0.474 0.1431075845
- 191 0.353 -0.637 1.236 -0.172 -0.116 0.474 0.1426990985
- 193 0.353 -0.635 1.236 -0.172 -0.116 0.474 0.1426940237
- 203 0.353 -0.635 1.294 -0.172 -0.116 0.474 0.1426287709
- 205 0.353 -0.635 1.267 -0.172 -0.116 0.474 0.1423279907
- 207 0.353 -0.635 1.270 -0.172 -0.116 0.474 0.1423240408
- 209 0.353 -0.635 1.269 -0.172 -0.116 0.474 0.1423230640
- 219 0.353 -0.635 1.269 -0.184 -0.116 0.474 0.1421965462
- 220 0.353 -0.635 1.269 -0.195 -0.116 0.474 0.1421919782
- 221 0.353 -0.635 1.269 -0.190 -0.116 0.474 0.1421769936
- 223 0.353 -0.635 1.269 -0.191 -0.116 0.474 0.1421761423
- 235 0.353 -0.635 1.269 -0.191 -0.120 0.474 0.1421721305
- 236 0.353 -0.635 1.269 -0.191 -0.118 0.474 0.1421696081
- 244 0.353 -0.635 1.269 -0.191 -0.118 0.532 0.1415484783
- 245 0.353 -0.635 1.269 -0.191 -0.118 0.542 0.1414569684
- 249 0.353 -0.635 1.269 -0.191 -0.118 0.548 0.1414469491
- 251 0.353 -0.635 1.269 -0.191 -0.118 0.550 0.1414460173
- 253 0.353 -0.635 1.269 -0.191 -0.118 0.549 0.1414459261
- 263 0.375 -0.635 1.269 -0.191 -0.118 0.549 0.1412665385
- 264 0.372 -0.635 1.269 -0.191 -0.118 0.549 0.1412527009
- 265 0.370 -0.635 1.269 -0.191 -0.118 0.549 0.1412521634
- 275 0.370 -0.646 1.269 -0.191 -0.118 0.549 0.1411436862
- 276 0.370 -0.648 1.269 -0.191 -0.118 0.549 0.1411432667
- 296 0.370 -0.648 1.269 -0.185 -0.118 0.549 0.1411159889
- 297 0.370 -0.648 1.269 -0.184 -0.118 0.549 0.1411140306
- 298 0.370 -0.648 1.269 -0.181 -0.118 0.549 0.1411132437
- 301 0.370 -0.648 1.269 -0.182 -0.118 0.549 0.1411126876
- 310 0.370 -0.648 1.269 -0.182 -0.122 0.549 0.1410933128
- 312 0.370 -0.648 1.269 -0.182 -0.124 0.549 0.1410913296
- 322 0.370 -0.648 1.269 -0.182 -0.124 0.566 0.1410126710
- 323 0.370 -0.648 1.269 -0.182 -0.124 0.564 0.1410103861
- 334 0.378 -0.648 1.269 -0.182 -0.124 0.564 0.1409838751
- 336 0.380 -0.648 1.269 -0.182 -0.124 0.564 0.1409838716
- 339 0.379 -0.648 1.269 -0.182 -0.124 0.564 0.1409830254
- 349 0.379 -0.646 1.269 -0.182 -0.124 0.564 0.1409792329
- 359 0.379 -0.646 1.266 -0.182 -0.124 0.564 0.1409789909
- 361 0.379 -0.646 1.267 -0.182 -0.124 0.564 0.1409778129
- 373 0.379 -0.646 1.267 -0.185 -0.124 0.564 0.1409715915
- 387 0.379 -0.646 1.267 -0.185 -0.125 0.564 0.1409707488
- 398 0.379 -0.646 1.267 -0.185 -0.125 0.570 0.1409646826
- 410 0.380 -0.646 1.267 -0.185 -0.125 0.570 0.1409638042
- 421 0.380 -0.645 1.267 -0.185 -0.125 0.570 0.1409606695
- 443 0.380 -0.645 1.267 -0.186 -0.125 0.570 0.1409603982
- 453 0.380 -0.645 1.267 -0.186 -0.124 0.570 0.1409583581
- 454 0.380 -0.645 1.267 -0.186 -0.123 0.570 0.1409575415
- 465 0.380 -0.645 1.267 -0.186 -0.123 0.571 0.1409573469
- Powell done niters = 5
- Computing relative cost
- 0 -25.0 -25.0 -25.0 0.995672
- 1 -25.0 -25.0 25.0 1.042601
- 2 -25.0 25.0 -25.0 1.011952
- 3 -25.0 25.0 25.0 1.001417
- 4 25.0 -25.0 -25.0 1.005375
- 5 25.0 -25.0 25.0 1.030164
- 6 25.0 25.0 -25.0 1.026341
- 7 25.0 25.0 25.0 1.008419
- REL: 8 0.140957 8.121942 1.015243 rel = 0.138841
- Number of iterations 5
- Min cost was 0.140957
- Number of FunctionCalls 467
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.789000 sec
- Parameters at optimum (transmm) 0.38005 -0.64469 1.26704
- Parameters at optimum (rotdeg) -0.18598 -0.12277 0.57063
- Final costs ----------------
- Number of surface hits 3047
- WM Intensity 56.9871 +/- 7.9749
- Ctx Intensity 69.4327 +/- 8.6816
- Pct Contrast 19.7210 +/- 13.7119
- Cost 0.1410
- RelCost 0.3084
- Reg at min cost was
- 0.999 -0.022 -0.034 -0.249;
- 0.032 -0.098 0.995 0.538;
- -0.026 -0.995 -0.098 -0.358;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/bbr.pass1.dat, type = 14
- Original Reg
- 0.999 -0.025 -0.025 -0.620;
- 0.022 -0.095 0.995 1.194;
- -0.028 -0.995 -0.094 -1.620;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.003 0.010 -0.372;
- -0.010 0.003 0.001 0.656;
- -0.002 -0.000 0.003 -1.262;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.418080
- Computing change in rh position
- Surface RMS Diff (mm) 1.349605 1.734044
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/transforms/tmp.bbregister.19392/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/bbr.pass1.dat
- subject sub002
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1376706176
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 -0.022 -0.034 -0.249;
- 0.032 -0.098 0.995 0.538;
- -0.026 -0.995 -0.098 -0.358;
- 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 1.005681
- 1 -25.0 -25.0 25.0 1.001206
- 2 -25.0 25.0 -25.0 1.012760
- 3 -25.0 25.0 25.0 1.019027
- 4 25.0 -25.0 -25.0 1.023239
- 5 25.0 -25.0 25.0 1.021860
- 6 25.0 25.0 -25.0 1.018151
- 7 25.0 25.0 25.0 1.018750
- REL: 8 0.160538 8.120674 1.015084 rel = 0.158153
- Initial costs ----------------
- Number of surface hits 306067
- WM Intensity 57.2975 +/- 8.3244
- Ctx Intensity 69.4291 +/- 8.7579
- Pct Contrast 19.2108 +/- 14.0392
- Cost 0.1605
- RelCost 0.1582
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1584 0.1584 0.0
- 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1579 0.1579 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1559 0.1559 0.0
- 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1548 0.1548 0.0
- 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1511 0.1511 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1491 0.1491 0.0
- 19 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.1464 0.1464 0.0
- 22 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.1457 0.1457 0.0
- 46 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.0000 0.1446 0.1446 0.0
- 49 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0000 0.1423 0.1423 0.0
- 293 0.0000 -0.1000 0.0000 0.1000 0.0000 0.1000 0.1422 0.1422 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1410 0.1410 0.0
- Brute Force --------------------------
- Min cost was 0.140957
- Number of iterations 729
- Search time 2.641000 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
- 8 -0.025 0.000 0.000 0.000 0.000 0.000 0.1604698779
- 11 -0.026 0.000 0.000 0.000 0.000 0.000 0.1604692307
- 12 -0.027 0.000 0.000 0.000 0.000 0.000 0.1604690775
- 20 -0.027 -0.085 0.000 0.000 0.000 0.000 0.1599344056
- 21 -0.027 -0.069 0.000 0.000 0.000 0.000 0.1598841461
- 22 -0.027 -0.066 0.000 0.000 0.000 0.000 0.1598820851
- 23 -0.027 -0.065 0.000 0.000 0.000 0.000 0.1598819801
- 31 -0.027 -0.065 -0.050 0.000 0.000 0.000 0.1594113639
- 32 -0.027 -0.065 -0.083 0.000 0.000 0.000 0.1593761960
- 33 -0.027 -0.065 -0.072 0.000 0.000 0.000 0.1593607907
- 34 -0.027 -0.065 -0.071 0.000 0.000 0.000 0.1593605731
- 35 -0.027 -0.065 -0.070 0.000 0.000 0.000 0.1593605096
- 44 -0.027 -0.065 -0.070 0.096 0.000 0.000 0.1582018373
- 45 -0.027 -0.065 -0.070 0.083 0.000 0.000 0.1581597755
- 46 -0.027 -0.065 -0.070 0.081 0.000 0.000 0.1581593829
- 48 -0.027 -0.065 -0.070 0.082 0.000 0.000 0.1581592468
- 56 -0.027 -0.065 -0.070 0.082 0.009 0.000 0.1581555923
- 57 -0.027 -0.065 -0.070 0.082 0.007 0.000 0.1581551333
- 68 -0.027 -0.065 -0.070 0.082 0.007 0.031 0.1580046776
- 70 -0.027 -0.065 -0.070 0.082 0.007 0.039 0.1580007565
- 71 -0.027 -0.065 -0.070 0.082 0.007 0.037 0.1579999205
- 72 -0.027 -0.065 -0.070 0.082 0.007 0.036 0.1579999029
- 82 -0.016 -0.065 -0.070 0.082 0.007 0.036 0.1579976067
- 83 -0.020 -0.065 -0.070 0.082 0.007 0.036 0.1579957129
- 84 -0.021 -0.065 -0.070 0.082 0.007 0.036 0.1579953629
- 86 -0.022 -0.065 -0.070 0.082 0.007 0.036 0.1579952922
- 93 -0.022 -0.051 -0.070 0.082 0.007 0.036 0.1579751893
- 94 -0.022 -0.050 -0.070 0.082 0.007 0.036 0.1579748305
- 95 -0.022 -0.049 -0.070 0.082 0.007 0.036 0.1579745553
- 104 -0.022 -0.049 -0.112 0.082 0.007 0.036 0.1576380933
- 105 -0.022 -0.049 -0.139 0.082 0.007 0.036 0.1576224577
- 106 -0.022 -0.049 -0.129 0.082 0.007 0.036 0.1576082843
- 115 -0.022 -0.049 -0.129 0.127 0.007 0.036 0.1575930703
- 116 -0.022 -0.049 -0.129 0.105 0.007 0.036 0.1574967914
- 117 -0.022 -0.049 -0.129 0.104 0.007 0.036 0.1574965506
- 127 -0.022 -0.049 -0.129 0.104 0.008 0.036 0.1574965050
- 138 -0.022 -0.049 -0.129 0.104 0.008 0.038 0.1574956748
- 147 -0.020 -0.042 -0.151 0.113 0.008 0.039 0.1574506786
- 148 -0.020 -0.042 -0.152 0.113 0.008 0.039 0.1574505847
- 150 -0.020 -0.042 -0.152 0.113 0.008 0.039 0.1574505287
- 161 -0.011 -0.042 -0.152 0.113 0.008 0.039 0.1574457183
- 162 -0.012 -0.042 -0.152 0.113 0.008 0.039 0.1574455433
- 163 -0.013 -0.042 -0.152 0.113 0.008 0.039 0.1574454586
- 173 -0.013 -0.040 -0.152 0.113 0.008 0.039 0.1574453159
- 174 -0.013 -0.039 -0.152 0.113 0.008 0.039 0.1574453127
- 184 -0.013 -0.039 -0.152 0.113 0.008 0.047 0.1574429504
- 185 -0.013 -0.039 -0.152 0.113 0.008 0.045 0.1574422983
- 203 -0.013 -0.039 -0.152 0.113 0.009 0.045 0.1574421157
- 215 -0.013 -0.039 -0.152 0.113 0.010 0.045 0.1574420488
- 226 -0.008 -0.039 -0.152 0.113 0.010 0.045 0.1574415627
- 227 -0.010 -0.039 -0.152 0.113 0.010 0.045 0.1574413323
- 236 -0.011 -0.040 -0.152 0.113 0.010 0.045 0.1574411857
- 237 -0.011 -0.041 -0.152 0.113 0.010 0.045 0.1574410506
- 251 -0.011 -0.041 -0.152 0.113 0.010 0.046 0.1574410163
- 268 -0.011 -0.041 -0.152 0.113 0.009 0.046 0.1574409780
- 282 -0.009 -0.043 -0.152 0.113 0.007 0.047 0.1574406570
- 288 -0.010 -0.042 -0.152 0.113 0.008 0.047 0.1574406306
- 294 -0.010 -0.042 -0.152 0.113 0.008 0.047 0.1574406169
- 312 -0.009 -0.042 -0.152 0.113 0.008 0.047 0.1574406043
- 341 -0.009 -0.042 -0.152 0.114 0.008 0.047 0.1574405976
- 351 -0.009 -0.042 -0.152 0.114 0.009 0.047 0.1574404797
- 352 -0.009 -0.042 -0.152 0.114 0.010 0.047 0.1574404247
- 356 -0.008 -0.044 -0.152 0.114 0.009 0.048 0.1574402747
- 360 -0.008 -0.043 -0.152 0.114 0.009 0.047 0.1574401378
- 361 -0.008 -0.043 -0.152 0.114 0.009 0.047 0.1574401359
- 367 -0.008 -0.043 -0.152 0.114 0.009 0.047 0.1574401258
- 394 -0.008 -0.042 -0.152 0.114 0.009 0.047 0.1574399686
- 415 -0.008 -0.042 -0.152 0.113 0.009 0.047 0.1574399435
- 430 -0.007 -0.043 -0.152 0.113 0.008 0.048 0.1574399122
- 435 -0.007 -0.043 -0.152 0.113 0.008 0.048 0.1574398981
- 437 -0.007 -0.043 -0.152 0.113 0.008 0.048 0.1574398809
- 475 -0.007 -0.043 -0.152 0.113 0.008 0.049 0.1574398589
- 492 -0.007 -0.043 -0.152 0.113 0.009 0.049 0.1574398442
- 513 -0.007 -0.043 -0.152 0.113 0.009 0.049 0.1574398301
- 514 -0.007 -0.043 -0.153 0.113 0.009 0.049 0.1574397932
- 569 -0.007 -0.043 -0.153 0.113 0.009 0.049 0.1574397637
- 635 -0.007 -0.043 -0.153 0.113 0.009 0.049 0.1574397566
- Powell done niters = 9
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.007105
- 1 -25.0 -25.0 25.0 1.000977
- 2 -25.0 25.0 -25.0 1.012423
- 3 -25.0 25.0 25.0 1.019748
- 4 25.0 -25.0 -25.0 1.024266
- 5 25.0 -25.0 25.0 1.022357
- 6 25.0 25.0 -25.0 1.018454
- 7 25.0 25.0 25.0 1.018845
- REL: 8 0.157440 8.124174 1.015522 rel = 0.155033
- Number of iterations 9
- Min cost was 0.157440
- Number of FunctionCalls 706
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 96.378000 sec
- Parameters at optimum (transmm) -0.00715 -0.04306 -0.15259
- Parameters at optimum (rotdeg) 0.11330 0.00929 0.04876
- Final costs ----------------
- Number of surface hits 306067
- WM Intensity 57.2881 +/- 8.2908
- Ctx Intensity 69.4207 +/- 8.7837
- Pct Contrast 19.2072 +/- 13.9822
- Cost 0.1574
- RelCost 0.1582
- Reg at min cost was
- 0.999 -0.022 -0.035 -0.256;
- 0.033 -0.096 0.995 0.495;
- -0.026 -0.995 -0.096 -0.509;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.999 -0.022 -0.034 -0.249;
- 0.032 -0.098 0.995 0.538;
- -0.026 -0.995 -0.098 -0.358;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 0.000 0.001 0.008;
- -0.001 -0.002 -0.000 0.043;
- 0.000 0.000 -0.002 0.151;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.158104
- Computing change in rh position
- Surface RMS Diff (mm) 0.145179 0.292914
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 -0.022 -0.035 -0.256;
- 0.033 -0.096 0.995 0.495;
- -0.026 -0.995 -0.096 -0.509;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.881;
- 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 -0.022 -0.035 -0.256;
- 0.033 -0.096 0.995 0.495;
- -0.026 -0.995 -0.096 -0.509;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub002
- RegMat ---------------------------
- 0.999 -0.022 -0.035 -0.256;
- 0.033 -0.096 0.995 0.495;
- -0.026 -0.995 -0.096 -0.509;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.001 -0.002 0.174;
- 0.001 0.999 0.033 0.490;
- 0.002 -0.033 0.999 0.098;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.699 -0.017 -0.022 39.493;
- -0.025 -0.064 -0.663 271.504;
- 0.016 0.663 -0.064 10.351;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 23:21:02 CEST 2013
- Ended at Thu Aug 8 23:34:14 CEST 2013
- BBR-Run-Time-Sec 792
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999032, 0.0218052, 0.0381938)
- j_ras = (0.0265301, 0.991428, 0.127932)
- k_ras = (0.0350768, -0.128822, 0.991047)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub002
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.001 -0.002 0.174;
- 0.001 0.999 0.033 0.490;
- 0.002 -0.033 0.999 0.098;
- 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/sub002/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 18670 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/sub002/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub002 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/sub002/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- 20389 bright wm thresholded.
- 326 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.orig...
- computing class statistics...
- border white: 305608 voxels (1.82%)
- border gray 333888 voxels (1.99%)
- WM (92.0): 93.4 +- 9.7 [70.0 --> 110.0]
- GM (76.0) : 74.6 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 48.3 (was 70)
- setting MAX_BORDER_WHITE to 114.7 (was 105)
- setting MIN_BORDER_WHITE to 61.0 (was 85)
- setting MAX_CSF to 35.6 (was 40)
- setting MAX_GRAY to 95.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 54.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 22.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=61
- mean inside = 92.7, mean outside = 69.6
- 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/sub002/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.02-->4.08) (max @ vno 105889 --> 106914)
- face area 0.33 +- 0.16 (0.00-->2.68)
- 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 2 with 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- deleting segment 6 with 12 points - only 0.00% unknown
- deleting segment 7 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 30 points - only 0.00% unknown
- deleting segment 10 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- 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 (0.06-->4.08) (max @ vno 106914 --> 105889)
- face area 0.33 +- 0.16 (0.00-->2.68)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4766040.0, rms=0.00
- rms = 2.29, time step reduction 1 of 3 to 0.250...
- rms = 0.59, time step reduction 2 of 3 to 0.125...
- rms = 0.08, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4766040.0, rms=0.000 (1.000%)
- positioning took 0.3 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 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 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 12 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 30 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- 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 (0.06-->4.08) (max @ vno 106914 --> 105889)
- face area 0.33 +- 0.16 (0.00-->2.68)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4766040.0, rms=0.00
- rms = 2.03, time step reduction 1 of 3 to 0.250...
- rms = 0.53, time step reduction 2 of 3 to 0.125...
- rms = 0.07, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4766040.0, rms=0.000 (1.000%)
- positioning took 0.3 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 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 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 12 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 30 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- 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 (0.06-->4.08) (max @ vno 106914 --> 105889)
- face area 0.33 +- 0.16 (0.00-->2.68)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4766040.0, rms=0.00
- rms = 2.29, time step reduction 1 of 3 to 0.250...
- rms = 0.59, time step reduction 2 of 3 to 0.125...
- rms = 0.08, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4766040.0, rms=0.000 (1.000%)
- positioning took 0.3 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 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 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 12 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 30 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- 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=4766040.0, rms=0.00
- rms = 2.03, time step reduction 1 of 3 to 0.250...
- rms = 0.53, time step reduction 2 of 3 to 0.125...
- rms = 0.07, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4766040.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 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 [81.30 212.70], gm=147.00+-21.90, and vertices in regions > 136.0
- 58159 surface locations found to contain inconsistent values (2108 in, 56051 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=522009.8, rms=0.27
- 001: dt: 0.5000, sse=493209.2, rms=0.258 (0.000%)
- 002: dt: 0.5000, sse=475991.9, rms=0.241 (0.000%)
- 003: dt: 0.5000, sse=467294.1, rms=0.228 (0.000%)
- 004: dt: 0.5000, sse=460228.8, rms=0.216 (0.000%)
- 005: dt: 0.5000, sse=455870.2, rms=0.206 (0.000%)
- 006: dt: 0.5000, sse=452957.9, rms=0.197 (0.000%)
- 007: dt: 0.5000, sse=451736.1, rms=0.189 (0.000%)
- 008: dt: 0.5000, sse=451005.8, rms=0.182 (0.000%)
- 009: dt: 0.5000, sse=451384.6, rms=0.176 (0.000%)
- 010: dt: 0.5000, sse=450710.3, rms=0.171 (0.000%)
- 011: dt: 0.5000, sse=450881.6, rms=0.167 (0.000%)
- 012: dt: 0.5000, sse=450864.9, rms=0.163 (0.000%)
- 013: dt: 0.5000, sse=450960.5, rms=0.160 (0.000%)
- 014: dt: 0.5000, sse=450526.3, rms=0.158 (0.000%)
- 015: dt: 0.5000, sse=450311.5, rms=0.156 (0.000%)
- 016: dt: 0.5000, sse=449499.1, rms=0.154 (0.000%)
- 017: dt: 0.5000, sse=449359.0, rms=0.152 (0.000%)
- 018: dt: 0.5000, sse=448337.1, rms=0.151 (0.000%)
- 019: dt: 0.5000, sse=448019.9, rms=0.150 (0.000%)
- 020: dt: 0.5000, sse=446818.6, rms=0.149 (0.000%)
- 021: dt: 0.5000, sse=446496.1, rms=0.149 (0.000%)
- 022: dt: 0.5000, sse=445546.1, rms=0.148 (0.000%)
- 023: dt: 0.5000, sse=444794.8, rms=0.148 (0.000%)
- 024: dt: 0.5000, sse=443847.1, rms=0.147 (0.000%)
- 025: dt: 0.5000, sse=443068.0, rms=0.147 (0.000%)
- 026: dt: 0.5000, sse=441568.9, rms=0.147 (0.000%)
- 027: dt: 0.5000, sse=441255.9, rms=0.147 (0.000%)
- 028: dt: 0.5000, sse=440194.6, rms=0.147 (0.000%)
- 029: dt: 0.5000, sse=439738.7, rms=0.147 (0.000%)
- 030: dt: 0.5000, sse=438530.6, rms=0.147 (0.000%)
- positioning took 4.1 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [81.30 218.70], gm=150.00+-22.90, and vertices in regions > 138.5
- 52018 surface locations found to contain inconsistent values (839 in, 51179 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=46531.7, rms=0.14
- 031: dt: 0.5000, sse=46095.0, rms=0.136 (0.000%)
- 032: dt: 0.5000, sse=47367.4, rms=0.122 (0.000%)
- 033: dt: 0.5000, sse=48962.1, rms=0.113 (0.000%)
- 034: dt: 0.5000, sse=50287.0, rms=0.107 (0.000%)
- 035: dt: 0.5000, sse=51504.4, rms=0.101 (0.000%)
- 036: dt: 0.5000, sse=52693.2, rms=0.096 (0.000%)
- 037: dt: 0.5000, sse=53796.8, rms=0.091 (0.000%)
- 038: dt: 0.5000, sse=54834.0, rms=0.087 (0.000%)
- 039: dt: 0.5000, sse=55909.9, rms=0.082 (0.000%)
- 040: dt: 0.5000, sse=56892.8, rms=0.079 (0.000%)
- 041: dt: 0.5000, sse=57865.9, rms=0.075 (0.000%)
- 042: dt: 0.5000, sse=58734.5, rms=0.072 (0.000%)
- 043: dt: 0.5000, sse=59589.5, rms=0.069 (0.000%)
- 044: dt: 0.5000, sse=60364.9, rms=0.066 (0.000%)
- 045: dt: 0.5000, sse=61180.8, rms=0.063 (0.000%)
- 046: dt: 0.5000, sse=61857.8, rms=0.061 (0.000%)
- 047: dt: 0.5000, sse=62521.8, rms=0.059 (0.000%)
- 048: dt: 0.5000, sse=63131.5, rms=0.057 (0.000%)
- 049: dt: 0.5000, sse=63755.6, rms=0.055 (0.000%)
- 050: dt: 0.5000, sse=64314.3, rms=0.053 (0.000%)
- 051: dt: 0.5000, sse=64831.8, rms=0.052 (0.000%)
- 052: dt: 0.5000, sse=65303.6, rms=0.050 (0.000%)
- 053: dt: 0.5000, sse=65795.2, rms=0.049 (0.000%)
- 054: dt: 0.5000, sse=66184.3, rms=0.048 (0.000%)
- 055: dt: 0.5000, sse=66592.6, rms=0.047 (0.000%)
- 056: dt: 0.5000, sse=66902.6, rms=0.045 (0.000%)
- 057: dt: 0.5000, sse=67230.8, rms=0.044 (0.000%)
- 058: dt: 0.5000, sse=67489.4, rms=0.043 (0.000%)
- 059: dt: 0.5000, sse=67699.3, rms=0.042 (0.000%)
- 060: dt: 0.5000, sse=67941.5, rms=0.041 (0.000%)
- positioning took 4.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [86.50 209.50], gm=148.00+-20.50, and vertices in regions > 137.7
- 12693 surface locations found to contain inconsistent values (2166 in, 10527 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=8662.8, rms=0.11
- 061: dt: 0.5000, sse=8608.5, rms=0.108 (0.000%)
- 062: dt: 0.5000, sse=8404.7, rms=0.101 (0.000%)
- 063: dt: 0.5000, sse=8253.4, rms=0.095 (0.000%)
- 064: dt: 0.5000, sse=8144.0, rms=0.090 (0.000%)
- 065: dt: 0.5000, sse=8071.3, rms=0.085 (0.000%)
- 066: dt: 0.5000, sse=8025.0, rms=0.081 (0.000%)
- 067: dt: 0.5000, sse=7979.6, rms=0.078 (0.000%)
- 068: dt: 0.5000, sse=7932.1, rms=0.075 (0.000%)
- 069: dt: 0.5000, sse=7886.0, rms=0.072 (0.000%)
- 070: dt: 0.5000, sse=7852.9, rms=0.069 (0.000%)
- 071: dt: 0.5000, sse=7827.4, rms=0.066 (0.000%)
- 072: dt: 0.5000, sse=7811.3, rms=0.064 (0.000%)
- 073: dt: 0.5000, sse=7807.6, rms=0.061 (0.000%)
- 074: dt: 0.5000, sse=7799.7, rms=0.058 (0.000%)
- 075: dt: 0.5000, sse=7793.7, rms=0.056 (0.000%)
- 076: dt: 0.5000, sse=7792.2, rms=0.054 (0.000%)
- 077: dt: 0.5000, sse=7789.9, rms=0.052 (0.000%)
- 078: dt: 0.5000, sse=7796.7, rms=0.050 (0.000%)
- 079: dt: 0.5000, sse=7797.1, rms=0.048 (0.000%)
- 080: dt: 0.5000, sse=7805.6, rms=0.046 (0.000%)
- 081: dt: 0.5000, sse=7812.1, rms=0.044 (0.000%)
- 082: dt: 0.5000, sse=7825.2, rms=0.042 (0.000%)
- 083: dt: 0.5000, sse=7830.3, rms=0.041 (0.000%)
- 084: dt: 0.5000, sse=7840.6, rms=0.039 (0.000%)
- 085: dt: 0.5000, sse=7851.9, rms=0.038 (0.000%)
- 086: dt: 0.5000, sse=7864.2, rms=0.037 (0.000%)
- 087: dt: 0.5000, sse=7874.2, rms=0.036 (0.000%)
- 088: dt: 0.5000, sse=7883.5, rms=0.035 (0.000%)
- 089: dt: 0.5000, sse=7891.8, rms=0.034 (0.000%)
- 090: dt: 0.5000, sse=7896.9, rms=0.033 (0.000%)
- positioning took 4.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [67.40 224.60], gm=146.00+-26.20, and vertices in regions > 132.9
- 50819 surface locations found to contain inconsistent values (12 in, 50807 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/sub002/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1409.3, rms=0.06
- 091: dt: 0.5000, sse=1323.0, rms=0.059 (0.000%)
- 092: dt: 0.5000, sse=1188.5, rms=0.050 (0.000%)
- 093: dt: 0.5000, sse=1139.4, rms=0.045 (0.000%)
- 094: dt: 0.5000, sse=1115.3, rms=0.042 (0.000%)
- 095: dt: 0.5000, sse=1094.7, rms=0.039 (0.000%)
- 096: dt: 0.5000, sse=1081.3, rms=0.037 (0.000%)
- 097: dt: 0.5000, sse=1070.9, rms=0.036 (0.000%)
- 098: dt: 0.5000, sse=1062.7, rms=0.035 (0.000%)
- 099: dt: 0.5000, sse=1055.0, rms=0.034 (0.000%)
- 100: dt: 0.5000, sse=1048.7, rms=0.033 (0.000%)
- 101: dt: 0.5000, sse=1043.7, rms=0.032 (0.000%)
- 102: dt: 0.5000, sse=1040.3, rms=0.031 (0.000%)
- 103: dt: 0.5000, sse=1037.3, rms=0.030 (0.000%)
- 104: dt: 0.5000, sse=1034.1, rms=0.030 (0.000%)
- 105: dt: 0.5000, sse=1031.7, rms=0.029 (0.000%)
- 106: dt: 0.5000, sse=1029.2, rms=0.029 (0.000%)
- 107: dt: 0.5000, sse=1027.3, rms=0.029 (0.000%)
- 108: dt: 0.5000, sse=1025.3, rms=0.028 (0.000%)
- 109: dt: 0.5000, sse=1024.1, rms=0.028 (0.000%)
- 110: dt: 0.5000, sse=1023.2, rms=0.028 (0.000%)
- 111: dt: 0.5000, sse=1022.6, rms=0.028 (0.000%)
- 112: dt: 0.5000, sse=1022.3, rms=0.027 (0.000%)
- 113: dt: 0.5000, sse=1021.3, rms=0.027 (0.000%)
- 114: dt: 0.5000, sse=1020.7, rms=0.027 (0.000%)
- 115: dt: 0.5000, sse=1020.2, rms=0.027 (0.000%)
- 116: dt: 0.5000, sse=1020.0, rms=0.027 (0.000%)
- 117: dt: 0.5000, sse=1019.9, rms=0.027 (0.000%)
- 118: dt: 0.5000, sse=1019.7, rms=0.027 (0.000%)
- 119: dt: 0.5000, sse=1019.5, rms=0.027 (0.000%)
- 120: dt: 0.5000, sse=1020.1, rms=0.027 (0.000%)
- positioning took 4.3 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.area.pial
- vertex spacing 1.03 +- 0.43 (0.08-->7.06) (max @ vno 111435 --> 111419)
- face area 0.41 +- 0.31 (0.00-->4.98)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 162178 vertices processed
- 25000 of 162178 vertices processed
- 50000 of 162178 vertices processed
- 75000 of 162178 vertices processed
- 100000 of 162178 vertices processed
- 125000 of 162178 vertices processed
- 150000 of 162178 vertices processed
- 0 of 162178 vertices processed
- 25000 of 162178 vertices processed
- 50000 of 162178 vertices processed
- 75000 of 162178 vertices processed
- 100000 of 162178 vertices processed
- 125000 of 162178 vertices processed
- 150000 of 162178 vertices processed
- thickness calculation complete, 605:965 truncations.
- 41783 vertices at 0 distance
- 118651 vertices at 1 distance
- 99728 vertices at 2 distance
- 36989 vertices at 3 distance
- 10002 vertices at 4 distance
- 2858 vertices at 5 distance
- 963 vertices at 6 distance
- 326 vertices at 7 distance
- 126 vertices at 8 distance
- 55 vertices at 9 distance
- 35 vertices at 10 distance
- 24 vertices at 11 distance
- 18 vertices at 12 distance
- 10 vertices at 13 distance
- 12 vertices at 14 distance
- 16 vertices at 15 distance
- 9 vertices at 16 distance
- 9 vertices at 17 distance
- 2 vertices at 18 distance
- 3 vertices at 19 distance
- 3 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.thickness
- positioning took 21.1 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub002 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/sub002/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- 19992 bright wm thresholded.
- 328 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.orig...
- computing class statistics...
- border white: 305608 voxels (1.82%)
- border gray 333888 voxels (1.99%)
- WM (92.0): 93.4 +- 9.8 [70.0 --> 110.0]
- GM (76.0) : 74.4 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.1 (was 70)
- setting MAX_BORDER_WHITE to 114.8 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.2 (was 40)
- setting MAX_GRAY to 95.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.3 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 92.8, mean outside = 69.2
- 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/sub002/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.03-->4.00) (max @ vno 107853 --> 109067)
- face area 0.33 +- 0.16 (0.00-->3.43)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 24 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 5 with 77 points - only 0.00% unknown
- deleting segment 6 with 5 points - only 0.00% unknown
- deleting segment 7 with 472 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 12 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.06-->3.75) (max @ vno 95101 --> 88276)
- face area 0.33 +- 0.16 (0.00-->3.43)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4946121.5, rms=0.00
- rms = 1.36, 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=4946121.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 24 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 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 77 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- deleting segment 6 with 472 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 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 (0.06-->3.75) (max @ vno 95101 --> 88276)
- face area 0.33 +- 0.16 (0.00-->3.43)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4946121.5, rms=0.00
- rms = 1.36, 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=4946121.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 24 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 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 77 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- deleting segment 6 with 472 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 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 (0.06-->3.75) (max @ vno 95101 --> 88276)
- face area 0.33 +- 0.16 (0.00-->3.43)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4946121.5, rms=0.00
- rms = 1.36, 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=4946121.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 24 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 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 77 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- deleting segment 6 with 472 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 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=4946121.5, rms=0.00
- rms = 1.36, 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=4946121.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- 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 [90.20 207.80], gm=149.00+-19.60, and vertices in regions > 139.2
- 55231 surface locations found to contain inconsistent values (4143 in, 51088 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=546910.6, rms=0.26
- 001: dt: 0.5000, sse=514420.6, rms=0.253 (0.000%)
- 002: dt: 0.5000, sse=495108.9, rms=0.238 (0.000%)
- 003: dt: 0.5000, sse=484468.0, rms=0.226 (0.000%)
- 004: dt: 0.5000, sse=476251.7, rms=0.215 (0.000%)
- 005: dt: 0.5000, sse=471347.7, rms=0.205 (0.000%)
- 006: dt: 0.5000, sse=467727.2, rms=0.197 (0.000%)
- 007: dt: 0.5000, sse=465879.7, rms=0.190 (0.000%)
- 008: dt: 0.5000, sse=463983.3, rms=0.184 (0.000%)
- 009: dt: 0.5000, sse=463124.8, rms=0.178 (0.000%)
- 010: dt: 0.5000, sse=462071.3, rms=0.174 (0.000%)
- 011: dt: 0.5000, sse=461640.4, rms=0.170 (0.000%)
- 012: dt: 0.5000, sse=460878.1, rms=0.167 (0.000%)
- 013: dt: 0.5000, sse=460294.7, rms=0.164 (0.000%)
- 014: dt: 0.5000, sse=459589.3, rms=0.161 (0.000%)
- 015: dt: 0.5000, sse=458760.2, rms=0.159 (0.000%)
- 016: dt: 0.5000, sse=458094.8, rms=0.157 (0.000%)
- 017: dt: 0.5000, sse=456837.6, rms=0.156 (0.000%)
- 018: dt: 0.5000, sse=456292.9, rms=0.155 (0.000%)
- 019: dt: 0.5000, sse=454951.7, rms=0.154 (0.000%)
- 020: dt: 0.5000, sse=453750.7, rms=0.153 (0.000%)
- 021: dt: 0.5000, sse=452578.5, rms=0.152 (0.000%)
- 022: dt: 0.5000, sse=451501.6, rms=0.152 (0.000%)
- 023: dt: 0.5000, sse=450358.2, rms=0.151 (0.000%)
- 024: dt: 0.5000, sse=449395.3, rms=0.151 (0.000%)
- 025: dt: 0.5000, sse=448435.2, rms=0.151 (0.000%)
- 026: dt: 0.5000, sse=447607.4, rms=0.151 (0.000%)
- 027: dt: 0.5000, sse=446392.5, rms=0.151 (0.000%)
- 028: dt: 0.5000, sse=445177.2, rms=0.151 (0.000%)
- 029: dt: 0.5000, sse=444232.2, rms=0.151 (0.000%)
- 030: dt: 0.5000, sse=443181.7, rms=0.151 (0.000%)
- positioning took 4.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [96.90 203.10], gm=150.00+-17.70, and vertices in regions > 141.1
- 39536 surface locations found to contain inconsistent values (5293 in, 34243 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=48162.5, rms=0.17
- 031: dt: 0.5000, sse=47843.2, rms=0.164 (0.000%)
- 032: dt: 0.5000, sse=48514.2, rms=0.154 (0.000%)
- 033: dt: 0.5000, sse=49544.4, rms=0.145 (0.000%)
- 034: dt: 0.5000, sse=50520.0, rms=0.139 (0.000%)
- 035: dt: 0.5000, sse=51356.9, rms=0.133 (0.000%)
- 036: dt: 0.5000, sse=52187.5, rms=0.127 (0.000%)
- 037: dt: 0.5000, sse=52974.3, rms=0.122 (0.000%)
- 038: dt: 0.5000, sse=53779.4, rms=0.117 (0.000%)
- 039: dt: 0.5000, sse=54595.2, rms=0.112 (0.000%)
- 040: dt: 0.5000, sse=55391.1, rms=0.108 (0.000%)
- 041: dt: 0.5000, sse=56232.5, rms=0.103 (0.000%)
- 042: dt: 0.5000, sse=56987.6, rms=0.099 (0.000%)
- 043: dt: 0.5000, sse=57735.5, rms=0.096 (0.000%)
- 044: dt: 0.5000, sse=58471.9, rms=0.092 (0.000%)
- 045: dt: 0.5000, sse=59184.1, rms=0.089 (0.000%)
- 046: dt: 0.5000, sse=59841.7, rms=0.086 (0.000%)
- 047: dt: 0.5000, sse=60478.3, rms=0.083 (0.000%)
- 048: dt: 0.5000, sse=61077.7, rms=0.080 (0.000%)
- 049: dt: 0.5000, sse=61640.4, rms=0.077 (0.000%)
- 050: dt: 0.5000, sse=62170.1, rms=0.075 (0.000%)
- 051: dt: 0.5000, sse=62651.6, rms=0.072 (0.000%)
- 052: dt: 0.5000, sse=63104.8, rms=0.070 (0.000%)
- 053: dt: 0.5000, sse=63556.2, rms=0.068 (0.000%)
- 054: dt: 0.5000, sse=63980.0, rms=0.066 (0.000%)
- 055: dt: 0.5000, sse=64350.8, rms=0.064 (0.000%)
- 056: dt: 0.5000, sse=64702.6, rms=0.062 (0.000%)
- 057: dt: 0.5000, sse=65028.9, rms=0.060 (0.000%)
- 058: dt: 0.5000, sse=65340.7, rms=0.058 (0.000%)
- 059: dt: 0.5000, sse=65644.1, rms=0.057 (0.000%)
- 060: dt: 0.5000, sse=65887.0, rms=0.055 (0.000%)
- positioning took 4.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [98.70 201.30], gm=150.00+-17.10, and vertices in regions > 141.4
- 29018 surface locations found to contain inconsistent values (3353 in, 25665 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=8328.2, rms=0.11
- 061: dt: 0.5000, sse=8281.1, rms=0.105 (0.000%)
- 062: dt: 0.5000, sse=8165.9, rms=0.100 (0.000%)
- 063: dt: 0.5000, sse=8081.1, rms=0.095 (0.000%)
- 064: dt: 0.5000, sse=8015.6, rms=0.091 (0.000%)
- 065: dt: 0.5000, sse=7958.8, rms=0.087 (0.000%)
- 066: dt: 0.5000, sse=7917.4, rms=0.084 (0.000%)
- 067: dt: 0.5000, sse=7877.4, rms=0.081 (0.000%)
- 068: dt: 0.5000, sse=7832.7, rms=0.078 (0.000%)
- 069: dt: 0.5000, sse=7793.2, rms=0.076 (0.000%)
- 070: dt: 0.5000, sse=7760.8, rms=0.073 (0.000%)
- 071: dt: 0.5000, sse=7732.4, rms=0.070 (0.000%)
- 072: dt: 0.5000, sse=7712.7, rms=0.068 (0.000%)
- 073: dt: 0.5000, sse=7694.1, rms=0.066 (0.000%)
- 074: dt: 0.5000, sse=7677.4, rms=0.064 (0.000%)
- 075: dt: 0.5000, sse=7670.8, rms=0.061 (0.000%)
- 076: dt: 0.5000, sse=7659.5, rms=0.059 (0.000%)
- 077: dt: 0.5000, sse=7652.7, rms=0.057 (0.000%)
- 078: dt: 0.5000, sse=7652.0, rms=0.056 (0.000%)
- 079: dt: 0.5000, sse=7650.8, rms=0.054 (0.000%)
- 080: dt: 0.5000, sse=7653.1, rms=0.052 (0.000%)
- 081: dt: 0.5000, sse=7652.5, rms=0.051 (0.000%)
- 082: dt: 0.5000, sse=7656.6, rms=0.049 (0.000%)
- 083: dt: 0.5000, sse=7659.6, rms=0.048 (0.000%)
- 084: dt: 0.5000, sse=7663.3, rms=0.047 (0.000%)
- 085: dt: 0.5000, sse=7671.2, rms=0.046 (0.000%)
- 086: dt: 0.5000, sse=7672.4, rms=0.044 (0.000%)
- 087: dt: 0.5000, sse=7676.2, rms=0.043 (0.000%)
- 088: dt: 0.5000, sse=7679.0, rms=0.042 (0.000%)
- 089: dt: 0.5000, sse=7682.3, rms=0.041 (0.000%)
- 090: dt: 0.5000, sse=7686.1, rms=0.040 (0.000%)
- positioning took 4.1 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [99.60 200.40], gm=150.00+-16.80, and vertices in regions > 141.6
- 23076 surface locations found to contain inconsistent values (1945 in, 21131 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/sub002/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1771.8, rms=0.08
- 091: dt: 0.5000, sse=1747.6, rms=0.080 (0.000%)
- 092: dt: 0.5000, sse=1658.7, rms=0.077 (0.000%)
- 093: dt: 0.5000, sse=1587.0, rms=0.074 (0.000%)
- 094: dt: 0.5000, sse=1524.1, rms=0.071 (0.000%)
- 095: dt: 0.5000, sse=1470.4, rms=0.068 (0.000%)
- 096: dt: 0.5000, sse=1430.8, rms=0.066 (0.000%)
- 097: dt: 0.5000, sse=1396.9, rms=0.065 (0.000%)
- 098: dt: 0.5000, sse=1361.2, rms=0.063 (0.000%)
- 099: dt: 0.5000, sse=1328.9, rms=0.061 (0.000%)
- 100: dt: 0.5000, sse=1299.4, rms=0.059 (0.000%)
- 101: dt: 0.5000, sse=1268.1, rms=0.058 (0.000%)
- 102: dt: 0.5000, sse=1240.5, rms=0.056 (0.000%)
- 103: dt: 0.5000, sse=1216.9, rms=0.054 (0.000%)
- 104: dt: 0.5000, sse=1194.4, rms=0.053 (0.000%)
- 105: dt: 0.5000, sse=1173.7, rms=0.052 (0.000%)
- 106: dt: 0.5000, sse=1156.3, rms=0.050 (0.000%)
- 107: dt: 0.5000, sse=1143.5, rms=0.050 (0.000%)
- 108: dt: 0.5000, sse=1126.4, rms=0.048 (0.000%)
- 109: dt: 0.5000, sse=1113.6, rms=0.047 (0.000%)
- 110: dt: 0.5000, sse=1101.2, rms=0.046 (0.000%)
- 111: dt: 0.5000, sse=1087.0, rms=0.045 (0.000%)
- 112: dt: 0.5000, sse=1074.1, rms=0.044 (0.000%)
- 113: dt: 0.5000, sse=1068.4, rms=0.044 (0.000%)
- 114: dt: 0.5000, sse=1058.0, rms=0.043 (0.000%)
- 115: dt: 0.5000, sse=1049.9, rms=0.042 (0.000%)
- 116: dt: 0.5000, sse=1041.9, rms=0.041 (0.000%)
- 117: dt: 0.5000, sse=1035.1, rms=0.041 (0.000%)
- 118: dt: 0.5000, sse=1032.2, rms=0.041 (0.000%)
- 119: dt: 0.5000, sse=1029.1, rms=0.040 (0.000%)
- 120: dt: 0.5000, sse=1021.9, rms=0.040 (0.000%)
- positioning took 5.3 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.area.pial
- vertex spacing 1.02 +- 0.43 (0.03-->6.15) (max @ vno 112370 --> 113418)
- face area 0.40 +- 0.31 (0.00-->6.32)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 161415 vertices processed
- 25000 of 161415 vertices processed
- 50000 of 161415 vertices processed
- 75000 of 161415 vertices processed
- 100000 of 161415 vertices processed
- 125000 of 161415 vertices processed
- 150000 of 161415 vertices processed
- 0 of 161415 vertices processed
- 25000 of 161415 vertices processed
- 50000 of 161415 vertices processed
- 75000 of 161415 vertices processed
- 100000 of 161415 vertices processed
- 125000 of 161415 vertices processed
- 150000 of 161415 vertices processed
- thickness calculation complete, 414:852 truncations.
- 38982 vertices at 0 distance
- 115625 vertices at 1 distance
- 101876 vertices at 2 distance
- 38318 vertices at 3 distance
- 10423 vertices at 4 distance
- 3020 vertices at 5 distance
- 953 vertices at 6 distance
- 338 vertices at 7 distance
- 142 vertices at 8 distance
- 71 vertices at 9 distance
- 45 vertices at 10 distance
- 24 vertices at 11 distance
- 17 vertices at 12 distance
- 15 vertices at 13 distance
- 11 vertices at 14 distance
- 4 vertices at 15 distance
- 14 vertices at 16 distance
- 13 vertices at 17 distance
- 18 vertices at 18 distance
- 12 vertices at 19 distance
- 7 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.thickness
- positioning took 22.0 minutes
- #--------------------------------------------
- #@# Surf Volume lh Fri Aug 9 00:19:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 00:19:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 00:19:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub002
- SUBJECTS_DIR is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- loading input data...
- computing distance to left white surface
- computing distance to left pial surface
- computing distance to right white surface
- computing distance to right pial surface
- hemi masks overlap voxels = 24
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Fri Aug 9 00:44:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002
- 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 sub002
- $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 sub002
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1487795 mm^3 (det: 1.309391 )
- Computing euler number
- orig.nofix lheno = -24, rheno = -20
- orig.nofix lhholes = 13, rhholes = 11
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 301051.478 299221.000 diff= 1830.5 pctdiff= 0.608
- rhCtxGM: 289136.374 288108.000 diff= 1028.4 pctdiff= 0.356
- lhCtxWM: 272836.406 272641.000 diff= 195.4 pctdiff= 0.072
- rhCtxWM: 274536.404 274780.000 diff= -243.6 pctdiff=-0.089
- SubCortGMVol 68034.000
- SupraTentVol 1234748.663 (1230966.000) diff=3782.663 pctdiff=0.306
- SupraTentVolNotVent 1206836.663 (1203054.000) diff=3782.663 pctdiff=0.313
- BrainSegVol 1384774.000 (1380497.000) diff=4277.000 pctdiff=0.309
- BrainSegVolNotVent 1351349.000 (1353893.663) diff=-2544.663 pctdiff=-0.188
- BrainSegVolNotVent 1351349.000
- CerebellumVol 148029.000
- VentChorVol 27912.000
- 3rd4th5thCSF 5513.000
- CSFVol 1249.000, OptChiasmVol 253.000
- MaskVol 1983181.000
- 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 15712 15712.156
- 4 5 Left-Inf-Lat-Vent 586 585.676
- 5 7 Left-Cerebellum-White-Matter 17221 17221.078
- 6 8 Left-Cerebellum-Cortex 58054 58054.180
- 7 10 Left-Thalamus-Proper 8295 8294.752
- 8 11 Left-Caudate 4520 4519.976
- 9 12 Left-Putamen 7471 7470.748
- 10 13 Left-Pallidum 2046 2046.089
- 11 14 3rd-Ventricle 1870 1870.421
- 12 15 4th-Ventricle 2631 2630.678
- 13 16 Brain-Stem 23971 23970.787
- 14 17 Left-Hippocampus 3975 3975.433
- 15 18 Left-Amygdala 1693 1692.719
- 16 24 CSF 1208 1207.880
- 17 26 Left-Accumbens-area 935 935.011
- 18 28 Left-VentralDC 4588 4588.086
- 19 30 Left-vessel 116 116.178
- 20 31 Left-choroid-plexus 1535 1534.951
- 23 43 Right-Lateral-Ventricle 7505 7504.894
- 24 44 Right-Inf-Lat-Vent 330 330.009
- 25 46 Right-Cerebellum-White-Matter 16869 16869.314
- 26 47 Right-Cerebellum-Cortex 59084 59084.398
- 27 49 Right-Thalamus-Proper 7459 7458.850
- 28 50 Right-Caudate 4785 4784.763
- 29 51 Right-Putamen 6567 6567.062
- 30 52 Right-Pallidum 1992 1992.300
- 31 53 Right-Hippocampus 4565 4564.830
- 32 54 Right-Amygdala 2235 2234.923
- 33 58 Right-Accumbens-area 818 818.038
- 34 60 Right-VentralDC 4389 4389.236
- 35 62 Right-vessel 136 136.460
- 36 63 Right-choroid-plexus 2202 2201.783
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 1484 1484.361
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 11 10.815
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 263 262.696
- 45 251 CC_Posterior 816 816.223
- 46 252 CC_Mid_Posterior 395 394.948
- 47 253 CC_Central 382 381.718
- 48 254 CC_Mid_Anterior 435 435.496
- 49 255 CC_Anterior 875 874.681
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Fri Aug 9 00:47:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002
- mri_aparc2aseg --s sub002 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub002
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/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/sub002/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 = 585527
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002
- mri_aparc2aseg --s sub002 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub002
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/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/sub002/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 = 585527
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Fri Aug 9 00:53:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002
- mri_aparc2aseg --s sub002 --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 sub002
- 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/sub002/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 8587 vertices from left hemi
- Ripped 8939 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/sub002/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 1131765
- Used brute-force search on 215 voxels
- Fixing Parahip LH WM
- Found 13 clusters
- 0 k 1.000000
- 1 k 1.000000
- 2 k 3.000000
- 3 k 1.000000
- 4 k 3.000000
- 5 k 1.000000
- 6 k 2483.000000
- 7 k 2.000000
- 8 k 1.000000
- 9 k 1.000000
- 10 k 5.000000
- 11 k 1.000000
- 12 k 1.000000
- Fixing Parahip RH WM
- Found 4 clusters
- 0 k 1.000000
- 1 k 1.000000
- 2 k 1.000000
- 3 k 2104.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002
- 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 sub002 --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 sub002 --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) = 1487795 mm^3 (det: 1.309391 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 301051.478 299221.000 diff= 1830.5 pctdiff= 0.608
- rhCtxGM: 289136.374 288108.000 diff= 1028.4 pctdiff= 0.356
- lhCtxWM: 272836.406 272641.000 diff= 195.4 pctdiff= 0.072
- rhCtxWM: 274536.404 274780.000 diff= -243.6 pctdiff=-0.089
- SubCortGMVol 68034.000
- SupraTentVol 1234748.663 (1230966.000) diff=3782.663 pctdiff=0.306
- SupraTentVolNotVent 1206836.663 (1203054.000) diff=3782.663 pctdiff=0.313
- BrainSegVol 1384774.000 (1380497.000) diff=4277.000 pctdiff=0.309
- BrainSegVolNotVent 1351349.000 (1353893.663) diff=-2544.663 pctdiff=-0.188
- BrainSegVolNotVent 1351349.000
- CerebellumVol 148029.000
- VentChorVol 27912.000
- 3rd4th5thCSF 5513.000
- CSFVol 1249.000, OptChiasmVol 253.000
- MaskVol 1983181.000
- 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 3831 3831.091
- 2 3002 wm-lh-caudalanteriorcingulate 3814 3814.421
- 3 3003 wm-lh-caudalmiddlefrontal 7714 7713.652
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2420 2419.591
- 6 3006 wm-lh-entorhinal 768 767.588
- 7 3007 wm-lh-fusiform 7569 7568.677
- 8 3008 wm-lh-inferiorparietal 12322 12321.860
- 9 3009 wm-lh-inferiortemporal 8571 8570.681
- 10 3010 wm-lh-isthmuscingulate 5372 5372.298
- 11 3011 wm-lh-lateraloccipital 8528 8528.081
- 12 3012 wm-lh-lateralorbitofrontal 7503 7503.267
- 13 3013 wm-lh-lingual 4903 4903.461
- 14 3014 wm-lh-medialorbitofrontal 4325 4325.258
- 15 3015 wm-lh-middletemporal 6471 6470.958
- 16 3016 wm-lh-parahippocampal 2538 2538.227
- 17 3017 wm-lh-paracentral 4375 4375.143
- 18 3018 wm-lh-parsopercularis 4565 4565.320
- 19 3019 wm-lh-parsorbitalis 1055 1054.862
- 20 3020 wm-lh-parstriangularis 3587 3586.795
- 21 3021 wm-lh-pericalcarine 2745 2745.437
- 22 3022 wm-lh-postcentral 8794 8793.513
- 23 3023 wm-lh-posteriorcingulate 4792 4792.316
- 24 3024 wm-lh-precentral 16555 16555.076
- 25 3025 wm-lh-precuneus 14226 14226.451
- 26 3026 wm-lh-rostralanteriorcingulate 2936 2935.535
- 27 3027 wm-lh-rostralmiddlefrontal 17354 17353.791
- 28 3028 wm-lh-superiorfrontal 23529 23528.588
- 29 3029 wm-lh-superiorparietal 14729 14729.310
- 30 3030 wm-lh-superiortemporal 10668 10667.562
- 31 3031 wm-lh-supramarginal 12458 12458.487
- 32 3032 wm-lh-frontalpole 363 362.975
- 33 3033 wm-lh-temporalpole 986 985.946
- 34 3034 wm-lh-transversetemporal 788 788.340
- 35 3035 wm-lh-insula 9377 9377.229
- 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 3423 3423.324
- 120 4002 wm-rh-caudalanteriorcingulate 4456 4456.400
- 121 4003 wm-rh-caudalmiddlefrontal 6650 6650.487
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2679 2679.339
- 124 4006 wm-rh-entorhinal 491 490.770
- 125 4007 wm-rh-fusiform 8395 8394.559
- 126 4008 wm-rh-inferiorparietal 15792 15791.956
- 127 4009 wm-rh-inferiortemporal 7249 7249.257
- 128 4010 wm-rh-isthmuscingulate 4719 4718.920
- 129 4011 wm-rh-lateraloccipital 8629 8629.347
- 130 4012 wm-rh-lateralorbitofrontal 6994 6993.996
- 131 4013 wm-rh-lingual 5119 5118.712
- 132 4014 wm-rh-medialorbitofrontal 4042 4041.585
- 133 4015 wm-rh-middletemporal 7586 7585.990
- 134 4016 wm-rh-parahippocampal 2100 2099.604
- 135 4017 wm-rh-paracentral 5214 5213.899
- 136 4018 wm-rh-parsopercularis 5190 5189.770
- 137 4019 wm-rh-parsorbitalis 1615 1614.556
- 138 4020 wm-rh-parstriangularis 4416 4416.242
- 139 4021 wm-rh-pericalcarine 2832 2831.788
- 140 4022 wm-rh-postcentral 9337 9336.530
- 141 4023 wm-rh-posteriorcingulate 4697 4697.445
- 142 4024 wm-rh-precentral 14892 14892.398
- 143 4025 wm-rh-precuneus 14794 14793.648
- 144 4026 wm-rh-rostralanteriorcingulate 2491 2491.264
- 145 4027 wm-rh-rostralmiddlefrontal 17783 17783.281
- 146 4028 wm-rh-superiorfrontal 22618 22617.725
- 147 4029 wm-rh-superiorparietal 14731 14730.840
- 148 4030 wm-rh-superiortemporal 7759 7759.177
- 149 4031 wm-rh-supramarginal 9730 9730.302
- 150 4032 wm-rh-frontalpole 326 325.656
- 151 4033 wm-rh-temporalpole 679 678.798
- 152 4034 wm-rh-transversetemporal 550 550.306
- 153 4035 wm-rh-insula 10108 10108.291
- 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 35120 35119.578
- 237 5002 Right-UnsegmentedWhiteMatter 38429 38428.828
- 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/sub002/label
- #--------------------------------------------
- #@# BA Labels lh Fri Aug 9 01:05:30 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 554
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4683
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 1056
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8965
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 229
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4306
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 597
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6580
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 970
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6754
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 566
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4636
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 2907
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 16496
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 525
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4706
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 1187
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4609
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 1546
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6187
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 2885
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 10999
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 464
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2482
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 153
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1352
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 127
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1141
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 361
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2453
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 36
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1540
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 159
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2155
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 454
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2773
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 185
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1734
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 1562
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 8597
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 212
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2124
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 529
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1680
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 1126
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4531
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 1278
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 4612
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178
- Number of reverse mapping hits = 89
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 602
- mri_label2label: Done
- mris_label2annot --s sub002 --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/sub002/label
- cmdline mris_label2annot --s sub002 --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 sub002
- 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/sub002/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 114791 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.BA.annot
- mris_label2annot --s sub002 --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/sub002/label
- cmdline mris_label2annot --s sub002 --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 sub002
- 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/sub002/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 134786 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub002 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 1253 711 2718 2.609 0.544 0.135 0.053 20 2.7 BA1
- 4876 3223 8595 2.437 0.522 0.123 0.038 53 7.0 BA2
- 972 665 1029 1.902 0.349 0.130 0.040 7 1.6 BA3a
- 2663 1714 4434 2.157 0.591 0.132 0.054 55 5.0 BA3b
- 1991 1045 4238 3.013 0.731 0.109 0.041 28 3.8 BA4a
- 1480 874 2695 2.893 0.635 0.108 0.033 10 2.2 BA4p
- 12325 8106 26696 2.700 0.634 0.140 0.087 1737 49.4 BA6
- 2711 1823 6359 2.947 0.443 0.124 0.038 32 4.0 BA44
- 3802 2583 7705 2.553 0.448 0.142 0.045 58 7.3 BA45
- 3763 2577 5581 1.963 0.473 0.153 0.072 77 11.8 V1
- 8404 5517 13735 2.208 0.500 0.160 0.062 170 19.6 V2
- 2089 1397 3463 2.302 0.354 0.132 0.042 27 3.7 MT
- 1058 711 2857 3.036 0.826 0.133 0.056 15 2.6 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub002 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 827 441 1808 2.652 0.498 0.137 0.074 16 1.9 BA1
- 2011 1317 3882 2.479 0.530 0.124 0.037 24 3.2 BA2
- 788 537 782 1.878 0.338 0.129 0.040 6 1.3 BA3a
- 1569 1048 2208 1.895 0.416 0.112 0.029 12 2.0 BA3b
- 2047 1038 4356 3.097 0.664 0.105 0.040 28 4.1 BA4a
- 1164 708 2018 2.797 0.649 0.110 0.031 7 1.6 BA4p
- 7098 4655 15293 2.681 0.666 0.145 0.112 1659 38.9 BA6
- 1711 1145 4114 2.995 0.412 0.129 0.041 21 2.6 BA44
- 1573 1067 3714 2.647 0.443 0.154 0.051 27 3.3 BA45
- 3994 2737 5997 1.968 0.464 0.155 0.072 82 12.5 V1
- 4118 2724 6480 2.108 0.468 0.173 0.073 95 10.8 V2
- 492 338 962 2.442 0.320 0.137 0.047 7 0.8 MT
- #--------------------------------------------
- #@# BA Labels rh Fri Aug 9 01:10:42 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 524
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4486
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 741
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 7428
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 238
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4218
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 534
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 5056
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 777
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 6524
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 455
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4928
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 2068
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 14324
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 2037
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 8949
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 2272
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 7627
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 1735
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 6462
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 3521
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 11537
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 918
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2850
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 96
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 848
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 109
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 985
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 236
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2924
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 62
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1760
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 324
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2507
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 213
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1601
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 164
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1653
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 1082
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 8041
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 416
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1428
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 403
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1581
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 1195
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4427
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 1542
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 4979
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub002 --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 = sub002
- 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/sub002/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415
- Number of reverse mapping hits = 131
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 399
- mri_label2label: Done
- mris_label2annot --s sub002 --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/sub002/label
- cmdline mris_label2annot --s sub002 --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 sub002
- 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/sub002/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 112972 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.BA.annot
- mris_label2annot --s sub002 --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/sub002/label
- cmdline mris_label2annot --s sub002 --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 sub002
- 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/sub002/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 135499 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub002 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 1079 641 2252 2.517 0.465 0.148 0.092 62 5.5 BA1
- 3722 2448 6016 2.276 0.433 0.125 0.034 41 5.4 BA2
- 1102 729 1080 1.878 0.405 0.133 0.041 10 1.8 BA3a
- 2526 1644 3649 1.894 0.506 0.129 0.038 29 4.3 BA3b
- 1922 1062 3806 2.878 0.532 0.111 0.050 36 4.4 BA4a
- 1368 880 2247 2.599 0.497 0.107 0.032 9 1.8 BA4p
- 9658 6509 21158 2.713 0.627 0.141 0.065 201 24.7 BA6
- 4658 3149 9257 2.655 0.429 0.117 0.036 51 6.9 BA44
- 5741 3937 11576 2.448 0.533 0.148 0.047 95 11.2 BA45
- 4265 2875 5905 1.927 0.476 0.160 0.099 85 11.9 V1
- 8997 5858 13897 2.199 0.514 0.163 0.061 235 22.9 V2
- 2730 1821 4560 2.454 0.429 0.130 0.040 32 4.4 MT
- 675 440 1860 3.033 0.850 0.152 0.085 10 2.2 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub002 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 704 411 1539 2.579 0.430 0.151 0.111 53 4.6 BA1
- 2069 1366 3451 2.262 0.463 0.122 0.034 25 3.0 BA2
- 950 640 868 1.845 0.362 0.133 0.038 7 1.5 BA3a
- 2040 1360 2678 1.757 0.435 0.117 0.032 17 2.7 BA3b
- 1137 631 2465 2.890 0.494 0.118 0.060 15 3.1 BA4a
- 1124 719 1977 2.736 0.515 0.103 0.033 7 1.7 BA4p
- 6082 4067 13144 2.669 0.665 0.141 0.066 121 16.5 BA6
- 1311 919 2984 2.745 0.389 0.125 0.041 17 2.1 BA44
- 1445 1001 3201 2.524 0.606 0.149 0.048 23 3.0 BA45
- 4045 2720 5592 1.951 0.474 0.158 0.102 80 11.4 V1
- 4633 3094 6701 2.071 0.493 0.176 0.071 164 13.8 V2
- 376 249 736 2.351 0.346 0.126 0.040 4 0.6 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 01:15:48 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub002 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub002.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1098 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub002 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 376 235 1293 3.372 0.598 0.150 0.082 9 1.2 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 01:16:04 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub002 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub002.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 809 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub002 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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
- 322 195 1036 3.334 0.808 0.183 0.099 8 1.7 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:53:55 CEST 2013
- Ended at Fri Aug 9 01:16:21 CEST 2013
- #@#%# recon-all-run-time-hours 14.374
- recon-all -s sub002 finished without error at Fri Aug 9 01:16:21 CEST 2013
|
