MCW AFNI UserMan ual

MedicalCollegeofWisconsin AnalysisofF unctionalNeuroImages

VersionDecember6

RobertWCoxPhD.

BiophysicsResearchInstitute MedicalCollegeofWisconsin WatertownPlankRoad MilwaukeeWI6

MedicalCollegeofWisconsin

SummaryMCWAFNIdisplaysthreedimensionalfunctionalneuroimagesoverlaidonto anatomicalreferencescansDatamaybetransformedtotheTalairachTournouxstereotaxicproportionalgridsystemImagesmaybegeneratedineachofthethreecardinal orthogonalplanesandswitchedamongmultiplefunctionalanatomicaldatavolumesAuxiliaryprogramsareprovidedtomanipulateandcombineDimagesetsTimedependent DimagesetsmayalsobestoreddisplayedandmanipulatedAnapplicationprogrammer interfaceisprovidedtoallowuserstoextendthefunctionalityofAFNIviaplugins.

DocumentThismanualdescribestheuseoftheAFNIprogramversionEarlier versionsxxaresupersededbythisversionbugsintheearlierprogramswillnolongerbe xedSeparatemanualsareprovidedfortheauxiliaryprogramsandfortheprogrammingofplugins.

DisclaimerThissoftwareanditsassociatedmanualsareprovidedASISandnowarranty fortheirusefulnessorcorrectnessforanypurposeismadeorimpliedbytheMedicalCollege ofWisconsinorbytheauthorThissoftwarehasnotbeenapprovedorevaluatedbythe UnitedStatesFoodandDrugAdministrationforanyclinicalapplication.

OwnershipandLicensetoUseThissoftwareanditsassociatedmanualsareCopyright bytheMedicalCollegeofWisconsinPermissionisgrantedtomakeuseofand tomakecopiesofthissoftwareanditsmanualsfornoncommercialresearchpurposesonly. Useofthesoftwareoritsmanualsbyforprotorganizationsisprohibitedwithoutprior writtenpermissionRedistributionofthisworkoranyderivedworkoutsideofthelicensed organizationisprohibitedwithoutpriorwrittenpermissionCopiesmaybemadewithinthe licensedorganizationwithoutseparatepermissionfromtheMedicalCollegeofWisconsin.

DistributionandRegistrationMCWAFNIisavailablefreeforresearchpurposesbutusers mustregisterwiththeMedicalCollegeofWisconsinForinformationsendanemailrequesttotheauthoratrwcoxmcweduwritetotheaddressaboveorseethenalpage ofthismanual.

AcknowledgementThisworkwasdevelopedwithinternalMCWfundsandwasalsopartly supportedbytheUnitedStatesNIHthroughgrantsMHandNS.

Con ten ts

Introduction3

WhatsNew4

Fundamentals6 Datasets6

Sessions9

ATourofAFNI 0 ResizingImageWindows9 ButtonClicksinaGraph0 MarkersfortheACPC AlignedTransformation7 Retransformationand RecreationofDatasets0

StartingUp0

ProgramControl1

ImageDisplay2

CrosshairsandtheView- point2

ColormapControls3

PositionControls4

DispControl4

SaveControl5

Montcontrol6

PopupMenu8

GraphDisplay9

Optmenu1

FIMmenu2

ViewingControls6

ViewModes6

DefineControls7

SwitchControls7

DefineMarkers7

MakingtheTransforma- tion9

TransformationtoStereo- taxicieTalairachCo- ordinates9

DefineFunction1

ThresholdSlider1

ColorPbar2

Options2

DefineDatamode3

Resampling3

DatasetOutputandIn- put3

ControllerLock4

Plugins5

Commandlineswitches5

TechnicalNotes7

mmaping7

machdeph8

XResourcesforAFNI8

FormulaforBkResampling8

Acknowledgements8

References9

MCWAFNIRegistrationForm0

In tro duction

AFNIisaninteractiveprogramforviewingtheresultsofDfunctionalneuroimagingItcan overlaytheusuallylowresolutionresultsoffunctionalbrainscansontohigherresolution structuralvolumedatasetsBymarkingducialpointsyoumaytransformthedatatothe proportionalgridstereotaxiccoordinatesofTalairachandTournouxTimedependent DvolumedatasetscanalsobecreatedandviewedAuxiliaryprogramsareprovidedfor combiningandeditingDandDtimefunctionaldatasets.

WiththisnewversionofMCWAFNImyintentionistoaddmanynewanalyticalcapabil

itiestothesoftwaresystemSomeofthesearefoundintheauxiliaryprogramsOthersare

foundintheAFNIprogramitselfinparticulartheinteractiveabilitytocomputefunctional

activationusingthecorrelationmethodThenewpluginscapabilityoersCliterateusers

theabilitytointegratetheirownanalyticaltoolsintoAFNIItismyhopethatothersites

willdevelopAFNIpluginsandsharethemwiththeFMRIcommunity. ! ThisdocumenthasbeenextensivelyrewrittenfromtheversionxmanualsMajornew

Whats

facilitiesinAFNIareoutlinedinthenextsection.

New�

! TheprogramrunsonUnixworkstationsusingtheXwindowingsystemandtheMotif ^ComputertoolkitforitsgraphicalinterfaceMinimumsystemrequirementstouseAFNIare2

requisites

MBRAMMBwillworkmuchbetterXRwithMotifanANSICcompiler, andenoughdiskspacetoholdtheDdatavolumesrequiredAFNIisdesignedtowork withorbitPseudoColorXvisualsAvisualofthistypemustbethedefaultvisual onthesystemusedtodisplayAFNITheprogramhasbeentestedonthefollowingsystems:

SGIIndigoworkstationsRandRCPUsrunningIRIXandIRIX.

HPworkstationsrunningHPUX.

IntelbasedLinuxsystems.

SunSPARCstationsrunningSolaris.

IthasnotbeentestedonotherplatformsItwillnotworkwithXRorMotifin particularitdoesnotworkunderSGIIRIXxTherearenoplanstoportittoradically dierentplatformssuchasMicrosoftWindowsortheAppleMacintosh.

AFNIisapowerfulprogramfordisplayandmanipulationoffunctionalneuroimageswith manyoptionsStudyofthismanualandexperiencewiththeprogramarebothrequired tomakefulluseofAFNISomeexperiencewithusingXisalsoveryusefulandwill beassumedinthismanual.

Nomenclature

IngeneralIrefertoMCWAFNIasthewholesoftwarepackageTheparticularprogram AFNIisattheheartofthepackageandisthesubjectofthismanualThepackage includesanumberofotherprogramsandtheprogramminginterfaceforcreatingplugins, bothofwhicharedocumentedelsewhere.

IfyoundMCWAFNIusefulandwishtorefertoitinapublicationtheappropriate citationis.

WhatsNew�

AtomicDatumTypes

PreviouslythedatastoredinanAFNIdatasethadtobebitsignedintegersshort datumThenewdatasetformatallowsforbitunsignedintegersbytedatum2 bitoatingpointsnumbersfloatdatumandbitcomplexnumberscomplex datumThepurposeofthebytedatumistoallowforcompactstorageofdatasets wheretherangehassucientprecisionThepurposeofthefloatdatumisto allowformorenaturalstorageofstatisticalquantitieswithouttheneedforrescalingto thelimitedrangeofvaluesallowedwithshortsButseeitembelowThepurpose ofthecomplexdatumistoeventuallyallowforunprocessedreconstructedimagesto bedirectlyimportedintoAFNI.

ScaleFactors

EachDsubbrickinadatasetcannowhaveaoatingpointscalefactorattachedto itThepurposeofthisistoallowdatatobestoredinthemorecompactbyteorshort formatsbutalwaystobeautomaticallyscaledtothecorrectunitswhenaccessedby anMCWAFNIprogramForexamplecorrelationcoecientscanstillbestoredas shortsbutwillbescaledbytotheirtruerange] beforebeingdisplayedorprocessedThenewinteractiveFIMutilityinAFNIdoes thisseeitembelowThenewtodcantakeasinputoatingpointvolumesand scalethemtoproduceshortorbytedatasetswiththeappropriatescalefactors) attached.

AuxiliaryStatisticalData

Therearethreenewtypesofdatasetstheficofittandfiftfunctionsficomeans functionalintensitywithcorrelationfittmeansfunctionalintensitywithttest� fiftmeansfunctionalintensitywithFtestThesearesimilarinconcepttothe fithimagesbutthethresholddatanowhasthestatisticalparametersegdegrees offreedomattachedthatallowcalculationofthesignicanceplevelWithsuch adatasetAFNIwillinteractivelydisplaythepvalueassociatedwiththechosen thresholdAtpresentonlyAFNIanddmgeneratedficodttestgeneratedfitt, anddANOVAgeneratedfiftdatasetshavethestatisticalparametersautomatically attachedUsingthenewtoditispossibletocreateyourowndatasetsofthesetypes ifyouprovidetheneededauxiliarystatisticalparameters.

DemiseofDatasetNameandShortLabel'

ThesevaluesarenolongerusedintodorAFNIThelenameofadatasetisnow usedfordisplayintheAFNIwindowtitlebarsandselectionchoosers.

Theoriginalpurposeofthenameandshortlabelvalueswastoassigndescriptionsto adatasetthatdidnotdependonthelenameThisisneededwhenonedatasetrefers toanotherwhichhappensduringthewarpondemandprocedureIfyourenameda datasetandiflenameswereusedastheinternalmethodofkeepingtrackofsuch referencesAFNIwouldgetconfusedTosolvethisproblemIhaveinsteadputinside eachdatasetsHEADleaninternallygeneratedidentiercodeThisisdesignedto beuniqueandindependentoflenamesWhenyourunanAFNIprogramonanold

datasetyouwillseeamessagethatitisgeneratinganewIDcodeTheseIDcodes arepseudorandomlygeneratedusingthecurrenttimeandmachinenameasseedsFor moreinformationseethepluginsmanual.

IfyouusetheUnixcommandcptocopyadatasetthenthenewdatasetwillhave thesameIDcodeastheoriginalAFNIwillnotruncorrectlyiftwosuchdatasets arereadintotheprogramToxthisyoucanusetheauxiliaryprogramdnewidto attachanewIDcodetoadataset.

DtimeDatasets

AFNInowsupportstimedependentDdatasetswhichIrefertoasDtimedatasets. Atpresentonlyanatomicaldatasetsmaybeusefullysetuptobetimedependent. Dtimedatasetsarecreatedwithtodusingthenewtimeztortimetzcommandlineswitches.

Dtimedatasetscanbeviewedintheimageviewingwindowsintheusualorthogonal slicesScrollingintimethroughtheseviewsisagoodwaytocheckforsubject movementTheycanalsobegraphedvstimesimilartotheprogramFD.

InteractiveFunctionalActivationAnalysis

AFNInowhastheabilitytoruntheequivalentofthemprogramonaDtime datasetproducingasoutputanewDficodataset.

ImageMontage

OneofthemostvisiblechangestoAFNIitselfistheadditionofthemontagedisplay ofanarrayofslicesfeaturetotheimageviewingwindowsThisisaccessedusingthe newMontbutton.

BigTalairachBox

ThesizeofthedefaultTalairachcoordinatesbrickhasbeenextendeddowninferior) bymmThisistomakesurethatthebrickincludestheentirecerebellumwhich isnotthecaseusingtheoldbrickdimensionstakenfromtheAtlas.

ThresholdResampling

Thetypeofinterpolationusedforfunctionaldatasetresamplingiscontrolledbythe ResammodebuttonintheDatamodecontrolpanelInAFNIxboththefunctional intensityfimandthethresholddatawereresampledusingthechosenmethod. InthisversionofAFNIthethresholddataegcorrelationcoecientisalways resampledusingtheNNmethodThisisbecausethresholdingwithaninterpolated nonlinearstatisticisasomewhatdubiousprocedure.

MultipleAFNIControllers

UsingtheNewbuttonyoucanopenupmultiplecontrollerwindowsinasinglerun ofAFNIThisallowsyoutoviewmorethanonedatasetatatimeUsingtheLock menuyoucanforcethecoordinatesofthedierentviewingwindowstobelocked togetherThisfeatureallowsyoutoscrollinunisonthroughmultipledatasets.

SessionDirectories

IfyoudontspecifyanydirectoriesonthecommandlinethenAFNIactsasifyou hadtypedthatisitwilltrytoreaddatasetsfromthecurrentdirectoryThe newRswitchwilltellAFNItoreadfromallsubdirectoriesofthegivensession directoriesrecursivelyUsingtheRescanbuttonsyoucanrereadsessionsThisis usefulifyouuseanauxiliaryprogramegdmergetocreateadatasetandthen wanttoimportitintoAFNI.

WritingManyDatasetstoDiskatOnce

AnewbuttonallowsyoutoselectmanydatasetsatonceforoutputtodiskThis makesitpossibletostartalongTalairachoutputsessionandthenleavethecomputer unattendedwhileitcomputeseachoutputBRIK.

3
This										section														explains																how								data											is					organized																		in				the							MCWAFNI																package																			The							two					indis
pensable																concepts																	are										datasets														and										sessions.
												Datasets
	!	The						fundamental																							unit												of			data									in							AFNI									is							the						dataset												one								or				more									D								bricks								of				imaging
Crucial information		datatogetherwithsomeauxiliaryinformationegaxesorientationcoordinatesofmarked
		ducial													points																							There														are									two							classes													of				datasets															anatomical																				and							functional															An
		exampleoftheformerwouldbeaSpoiledGRASSMRIscan																																																											Anexampleofthelatterwould
		betheresultsofcrosscorrelatingafunctionalMRIFMRItimecourseofimages																																																											When
		youcreateadatasetusingthetodprogramyoumustspecifywhetheritisanatomicalor
		functionalinnature																																					When												you									areusingAFNIatany																																							giventimeyou																									willb							e			displaying
		one					anatomical																							dataset															as					the								grayscale																	underlay																	and					possibly															one											functional															dataset
		as		the									false										color									overlay.
		Within																the										class								of						anatomicaldatasets																																						tod									provides													you					with						a						list							of			possible												types
		egSpoiledGRASSEchoPlanarMRAngiogram																																																											Atpresentallanatomicaltypes
		of	datasets																		are								treated															identically																						The								only									reason												for			choosing												a					particular																	anatomical
		type							is					to					remind													yourself																	of					the									datasets																origin.
	!	Anatomicaldatasetsmayb																																																			e			intheDortheDtimeformat																																																												TheDformatstores
Dtime		one				value											p			e		r			voxel												The										Dtimeformatstores																																											aseries											of				values						p			e				r			voxel									This									can				b	e
		usedtostoredallthedatafromaDFMRIimagingrun																																																											Theauxiliaryprogramdmor
		the			internal																		AFNI											FIM											capability																				can					b		e				used											to				produce												functional																			activation														datasets
		from									Dtime																		datasets.
		Withinthe																									class								of						functionaldatasets																																				there											are						presently												ve				types.
		fim																								FunctionalIntensity
																										onevalueisstoredp																																											er				voxel

fithFunctionalIntensityThreshold twovaluesarestoredpervoxel: therstisintensitydenedarbitrarily� thesecondisthresholdwhichisaeitheraoatingpointnum

berbetweenandorabyteintegerbetween0 andwhichcanbeusedtoselectwhichvoxelsareconsideredactive.

ficoFunctionalIntensityCorrelation twovaluesarestoredpervoxel: therstisintensity� thesecondisacorrelationcoecientbetweenand,

whichcanbeusedtoselectactivevoxelsatagivensignicance pvalue.

fittFunctionalIntensityttest twovaluesarestoredpervoxel: therstisintensity� thesecondisatstatisticwhichcanbeusedtoselectactive'

voxelsatagivensignicance. fiftFunctionalIntensityFtest twovaluesarestoredpervoxel: therstisintensity� thesecondisanFstatisticwhichcanbeusedtoselectactive' voxelsatagivensignicance.

ByintensityImeanasignednumberindicatingtheleveloffunctionalactivityineachvoxel. IconsiderthefithdatasettypetobeobsoleteItisretainedforcompatibilitywithAFNI versionxThelatterthreefunctionaltypesdierfromthefithtypeinthatAFNIknows howtostatisticallyinterpretthesecondvalueattachedtoeachvoxel. ! Thevaluesstoredateachvoxelcanbeanyofthefollowing:

Atomic datum

byteatypedefforunsignedchar

shortbytesignedint floatsingleprecisionbytes complexastructcontainingtwofloatsbytes

IrefertothesetypesastheatomicdatumtypesofadatasetFloatandcomplexdatasets maynotbeportablebetweenCPUarchitecturesAlsoshortdatasetsmayneedtobe byteswappedifthelesaremovedtoadierentcomputerSpecicallyIntelCPUsare reversedfrommostotherUnixsystemssothatshortbricklescreatedonanSGIsystem wouldhavetobebytereversedbeforetheycouldbeusedonanIntelbasedsystemThe auxiliaryprogramswapcanperformthisfunction.

FormostpurposestheshortatomicdatumisthemostusefulEachDbrickwithina shortorbytedatasetcanhaveaoatingpointscalingfactorattachedsothattheAFNI programswillinterpretthevaluestoredasfactorvoxelvalue.

Datasetsarestoredintwo																																																																		le							s							theheader																													andbrick																						les												Theheaderlecontainsallthe
auxiliaryinformationabout																																																														a					dataset																														stored														in				an											ASCII															format														The							brick										le										contains
onlytheactualDvolumedata																																																														FordetailsonthestorageseetheAFNI																																																							pluginsmanual.
	!	The													les																in									a									dataset																									have																	highly																			structured																										names																	and								these													names											should																	not										b	e
Filenames		casuallyaltered																																													or											AFNI																		willnot																							b				e				ableto																					read													them												The										general														formof														the										dataset
		lenames																					is							prefixviewNAME																																																															where																prefix																						is						to					b			e			suppliedby																						the								user											you															and
		presumably																												would																								b						e						used														to									indicate																								the											type										of									data										stored														in					the						le						eg													spgr														for
		SpoiledGRASS																																														func																				for							functional																														intensityetc																																						The										view																	code							indicates																		the											origin
		of		the								data																and																is										assignedby																																						AFNI																				the									possibilities																											are:
		orig																		fororiginaldatauntransformedbyAFNI																																																																)
		acpc																		fordatasetswhichhaveb																																																																e		e						n				alignedtotheACPCline
		tlrc																		fordatasetswhichhaveb																																																																e		e						n				transformedtotheTalairachTournouxgrid
		Datasets																		in									the													acpc																											and										tlrc																			views																		would															normally																					b		e			created																by							AFNI													orig																les
		would										b				e				created																														by															tod																The																NAME																					sux													is						HEAD															for							the									header													le							and										is							BRIK
		for						the								brick																		le.
		Onereasonforsplittingtheauxiliaryinformationfromthevolumedataineachdatasetis
		foreciencyofaccesstothebrick																																																																le															Anotherreasonisthatinanemergencytheauxiliary
		informationis																																	stored																														in						ASCII																				formand																										so								can							b			e					edited															manuallythisrequires																																												extreme
		care											A											third																	reason																													is			that															when																transformed																															datasets																				acpc																and						tlrc													are									created,
		theirbrick																						le								s					m								a						ybedeletedlatertosavediskspaceaslongasthetransformedheader
		lesandtheorig																																																							bricklesexist																																													AFNI																		can										recreatethe																										transformeddata.
		OncerawimageshavebeenputintotheAFNI																																																																datasetformattheyarenolongerneeded
		for					any										of									the												programs																																		described																												herein																							It						is				always																	possible																			using												AFNI											or								fromd)
		to				extract																			images																											out															of					the												D											data													brick																		although																					you								may									then											have								to					convert																			them
		into							whatever																											format																															you										desire.
		If								you											choose																											to													rename																						the											pair												of									les												that												make												up							a				dataset																	the							only										part														you
		should												touch																			is										the																				prex																			If									you										alter																		the								view																	or					NAME													parts														AFNI											will									probably
		refuse									to											read																	the																les																at							all.
	!	Not											all												datasets																															will															have														a								BRIK																	le												AFNI																is							capable															of						transforming																							data														from											a
Warpondemand		parent																dataset																									as													needed																						for												image																	display																						If						the											necessary																			transformation																													eg														from
		origtotlrc																																									is										a						vailablethenthechilddatasetegthetlrcdatasetneednothave
		aBRIK																	leitcan																																											b			e				warpedondemandfordisplay																																																							Normallyorig																												datasets																				donot
		haveawarpparentdatasetsotheymusthaveaBRIKle																																																																Anexceptiontothisrulecan
		b	e		created																						with																			the																		auxiliary																							program																											ddup)
		AtthistimenoprogrambutAFNI																																																																itselfcandealwithwarpondemanddatasets																																																							That
		isalltheauxiliaryprogramsandpluginsmustdealwithactualdatasetBRIKs.


	!	Allofthedatasetlesthatgotogethershouldb																																																															e			gatheredintoasingledirectory																																																					Bygo
Crucial information		togetherIspecicallymeanthosedatasetsgatheredduringthesamescanningsessionona
		singlesubject																							Aftertheirpositionsandorientationsaresetupintodallthesedatasets
		arepresumedtob																																e						alignedtooneanother																																																		If								this							isnot									the							case												then					the						imagesmaking
		upthedatasetsshouldbe																																																		registered																			b				eforeentryintotod																																							Theauxiliaryprogramimregmay
		b	e	useful														for					this												purpose																									Alternatively																													the								program														AIR								from											UCLA										might											b		e			needed.
		AIR					is					availableat																											httpbishopwloniuclaeduAIRindexhtml.
		A						directory																			containing																														datasets																	is							called												a						session													The											hierarchy																of				les									that							make
		up				a			session														is									pictured																							below:
																																																							session																																																								toplevel																								directory
																																																																								\
																																																																								\
		/																																																															\|																	\
																																	header																										header																			header																																	actual																data										files
																																	brick																										brick																			brick
																																	header																										header																			header
																																	brick																										brick
		Itispermissibletosaveotherlesegtheoriginalimagelesinthesessiondirectory
					these										les									will													simply																			b			e					ignored																by							AFNI.
		AFNI														takes															as						input																	a					collection																				of					sessions																specied																	by							their												directory													names											and
		allowsyoutoswitch																																								b			e			tweenthemandbetweentheirconstituentanatomicalandfunctional
		datasets															It					is				importantto																																					understand																							the								dataset												concepts																			le						structure															and								directory
		hierarchy																	described																								and											depicted																			above.
	!	Sessions																		are										referred																					to							by									the						topleveldirectory																																			name										under														which									all				their										datasets
Command linenames		reside											An							individual																											dataset																				is			referred																		to			onauxiliary																									program																		command														linesby													the
forsessions		name								of				its							header																				le									the												name										of					its								brick											le							or				justby															the							prefixview																					part								of			the
datasets		lenamesforexample,
		decfuncacpcHEAD																																																															decfuncacpcBRIK																																																										decfuncacpc
		would									allrefer																	to								the										same															dataset															residing																ina									given								session																	directory.
		Bymovingtothedirectoryabovethesessiondirectory																																																															y				oucansaveandcompressallthe
		lesinasessionusingthecommand
		tar																																				cvf											session																										directory																											gzip								v										sessiontgz
		This						presumes																					that															you									have													the							GNU										gzip												compression																				utility													installed														on					your										system.
		Thecommandtouncompressandrestorefromthecompressedarchivewouldb																																																															e
		gzip																																																															dc									sessiontgz																														tar									xvf

AT ourof AFNI

Thebestwaytolearntheprogramistoreadthistourthroughandthensitdownwith theprogramandtryitout.

StartingUp

ThecommandlinetorunAFNIisquitesimple:

afnisessionsession.

HeresessionisthenameofasessiondirectorytoreadinAlltheDdatasetsunder eachnamedsessiondirectorywillbereadinIfnosessionsarespeciedonthecommand linethecurrentworkingdirectorywillbeusedCommandlineoptionsforAFNIwill bediscussedinalatersection)

ForAFNItobeabletouseasessionitmustcontainatleastoneanatomicaldataset DorDtimeIfnoneareavailabletheauxiliaryprogramddupcanbeusedtocreate awarpondemandcopyofafunctionaldatasetAlternativelyyoucouldusetherstimage fromtheFMRItimecourseineachslicetoformananatomicaldatasetbutaseparate higherresolutionscanwillbemoreusefulandlookbetterAtanygivenmomentinAFNI, youareviewingonegivenanatomicaldatasetandpossiblyonegivenfunctionaldataset. Controlsaresuppliedtoletyouswitchamongsessionsandamongdatasetswithinsessions.

Ausefulmodelistothinkofeachsessionasbeingorganizedinatwodimensionallayout:

ViewType

origacpctlrc

anatX X

prefixangioX O

funcX O

AcrossthetopistheviewtypeOriginalACPCalignedorTalairachDownisthe datasetprexXsmarkdatasetsthatactuallyexistondiskInthesampleabovethe anatoriginaldatahasalsobeentransformedtotheACPCalignedviewusingthemarker driventransformationdescribedlater.

WhenAFNIstartsalltheotherdatasetsinthissessionwillalsohaveACPCaligned viewversionsmadeinternallyintheprogramtheseareindicatedbyOsinthetableabove. NoHEADleswillbewrittenforthesedatasetsatthistimeThesedatasetswillbewarpondemanduntilandunlessyouwriteouttheBRIKlesusingoneoftheWritebuttons describedlaterThetransformationfromorigtoacpcintheanatdatasetstoredinthe HEADlewillbeappliedtotheotherdatasetsintheorigviewThesefollowerdatasets arewhatmakesAFNIworkandeasytouseWhentheanattransformationfromacpcto tlrcisdenedwhentheXisplacedatthetopofthethirdcolumnthenalltheother datasetsinthissessionwillagainfollowalongOswillllintherestofthethirdcolumn.

MCWAFNI2.00 { Dec6

Forthistobepossibleitisnecessarythatthecorrectgeometricalrelationshipbetween thedatasetscomprisingasessionbeestablishedwhentodisrunthatistheimportof gettingtheaxesorientationsandoriginscorrectintod.

! AFNIisalsocapableofdirectlyreadinginanddisplayingasetofimagelesUsethe

afniim

commandafnihelpfordetailedinstructionsonhowtodothisInthismodenoneof thecontrolsfordatasettransformationfunctionaloverlayetcareavailable. AfteryoustartAFNIacontrolwindowopensontheXscreen:

AFNIcontrollerandimageviewingwindows

ProgramControl

Atthelowerleftofthecontrolpanelarefourbuttonswhichcontrolvariousglobalprogramfunctions:

NewThisbuttonwillopenupanewAFNIcontrollerwindowInthiswayitispossibleto openupimageviewersonmorethanonedatasetorsessionatatimeAmaximum ofcontrollerwindowscanbeopenatonceTherstcontrollerwindowandits childrenaremarkedwithAintheirtitlebarsthesecondismarkedwithBandso forth.

ViewsThisbuttonwillopenandclosethecontrolpanelstotherightoftherstcolumn ofthecontrollerwindowtherstsuchcontrolpanelstartswithOriginalViewinthe gureaboveThisfunctionallowsyoutosavesomescreenspacewithouticonifying thecontrollerwindow.

BHelpThisbuttonallowsyoutopopupahelpwindowformostcontrolswithinAFNI. PressingBHelpwillcausethemousecursortochangetoasmallhandshapePressing

MCWAFNI2.00 { Dec6

mouseButtonwhilethehandisoveranAFNIcontrolwillpopupahelpwindowfor thatcontrolClickingButtoninsidethehelpwindowwilldismissit.

ButtonhelpisimplementedasahelpcallbackinMotifIfyourterminalkeyboard isappropriatelysetupthenpressingtheMotifHelpkeyoftenFwhilethemouse cursorisoverabuttonorotherwidgetwillalsocausethehelpwindowforthatwidget topopup.

doneThisbuttonwillclosethecontrollerwindowwhenpressedtwicewithinseconds. IfthisistheonlycontrollerwindowrunningAFNIwillalsoexitFormoredetails, tryusingBHelpondone)

TheMCWlogowillappearintheemptyspacejusttotherightofthesefourbuttonswhen theprogramisdoingsomeoperationthatispotentiallytimeconsumingAtthesametime, themousecursorwillchangetoawatchshapeWhenthetimeconsumingoperationisover, thelogowillberemovedandthecursorwillchangebacktoitsusualarrowshape.

AtrickIsometimeusetovisuallygrabattentionwhenalengthytaskisunderwayisto clicktheSwapbuttoninanimagewindowThiswillturntheimagestoreversevideowhen theprogramcatchesupwithyouThenSwapagainandproceed.

ImageDisplay

Therstcolumnofthecontrollerwindowcontainsthecontrolsthatenableyoutoopenthe imageviewingwindowsthethreeImagebuttonsThewindowsopenseparatelyonthe XdisplayscreenandmaybepositionedandresizedindependentlyAlittlepracticeis neededtodecideuponagoodlayoutschemeforthesewindowsThereasonAFNIdoesnot denetheirlocationsandsizesisthatitisoftendesirableexpandonewindowtolookat somedetailsandtemporarilycoveruptheotherwindows.

WhenanImagebuttonishighlightedininvertedcolorsthismeansthatitswindowisalreadyopenPressingthebuttonagainwillbringthatwindowtothetopofthedisplaythis isusefuliftheimageviewingwindowishiddenbeneathsomeotherwindoworisiconied.

AnimageviewingwindowcanbeclosedbyusingtheDonebuttonalongitsbottomedge. AlternativelythewindowmanagerCloseorDeletefunctionmaybeused.

CrosshairsandtheViewpoint

Youcanhaveuptothreeimageviewingwindowsopenatanygiventimeoneaxialone

sagittalandonecoronalIntheaxialandcoronalwindowsimagesaredisplayedwith ! thesubjectsleftonthescreenrighttheusualradiologicalconventionThesewindows

Leftis

areorthogonalslicesthroughtheDdatasetThecoloredcrosshairsthatoverlayeach

Right!

imagemarktheslicesthatarevisibleintheotherimagewindowsThepointatwhichthe crosshairsintersectiscalledtheviewpoint.

IntheupperlefthandcorneroftheAFNIcontrollerwindowaredisplayedthecoordinates ofthecurrentviewpointThesecoordinatesarepresentedintheDICOMstandardorder:

xaxisisRightnegativetoLeftpositive) yaxisisAnteriornegativetoPosteriorpositive)

zaxisisInferiornegativetoSuperiorpositive)

InternallyAFNIusesDICOMcoordinatestokeeptrackofeverythingHoweverAFNI cannotreadDICOMles)

ThebuttonXhairsjustunderthecoordinatedisplayallowsyoutoswitchbetween3 modesforcrosshairdisplay:

OffCrosshairsarenotdisplayed.

SingleAsinglecrosshairisdisplayedatthexyzcoordinatesoftheviewpoint' iethepointwhosecoordinatesaregivenintheupperleftcorner.

MultiIfamontageofslicesisdisplayedinanimageviewingwindowthentheorthogonal sliceswillhavecrosshairsindicatedforallthemontagedslicesThisisusefulfor indicatingtheanatomicallocationofthemontagelayout.

Youmaychangethecrosshaircolorandcentralgapwiththeselectorsjustunderneaththe

XhairsbuttonThecolorsavailableforthevariousoverlaysarebuiltintoAFNIbutcan bealteredbyappropriatechangestoyourXdefaultsle.

Ifyouclicktheleftmousebuttonwhilethecursorisinanimagewindowthenthe crosshairswillimmediatelyjumptothatlocationThiswillusuallymeanthattheothertwo windowswilldisplaynewslicesTheimagewindowsarealwayslinkedinthisfashion.

TheIndexcontrolontheAFNIcontrollerwindowisusedtocontrolthetimeindexof theviewpointThiscontrolisonlyactiveifthecurrentanatomicaldatasetisintheDtime formatThetimeindexcanalsobecontrolledinagraphviewer)

ColormapControls

AttherightofeachimagewindowisasetofbuttonsthatareusedtocontroltheX1 colormapassignedtothewindowsFromtoptobottomthesecontrols

ColrChangefromgrayscaletoacolorscaleandback.

SwapInvertthegrayscaleorcolorscaleswapitendforend.

NormReturnthecolormaptoitsinitialstateafteryoumessitup.

Changethecontrastofthegrayscaleamultiplicativechangetotheintensityofeach pixel.

bChangethebrightnessofthegrayscaleanadditivechangetotheintensityofeach pixel.

Rotatethegrayscaleorcolorscale.

gChangethecorrectionfactorforthegrayscale.

iChangethefractionoftheviewingwindowtakenupbytheimage.

Youmayhavetodragtheviewingwindowstobelargerthantheirinitialsizessothatthese andtheothercontrolsdontobscureeachotherChangingthecolormapinoneviewing windowaectsalltheotherwindowsfromthesameAFNIprocess.

PositionControls

BeloweachimageisasliderthatindicatestheimagenumberinthecurrentsequenceBy draggingthisslideryoucanmovethroughtheslicestoanygivenslicenumberIndoingso, youwillalsomovethecrosshairsintheothertwoimagewindows.

Atthelowerrightoftheimagewindowisanarrowpadoffourarrowsarrangedina NEWSpatternplusacentralbuttonClickingononeofthearrowswillcausethe crosshairviewpointtomoveonevoxelinthedirectionpointedbythearrowinthatwindow. Clickingonthecentralunlabeledbuttoncausesthecrosshairgaptocloseclickingthis buttonagaincausesthegaptoopenupagainThisisveryusefulwhenpositioningthe crosshairspriortosettingananatomicalmarker.

ImageviewerDispandMontcontrolpanels

DispControl

Thisbuttonopensupacontrolpanelpicturedabovethatletsyouchangehowtheimages willbedisplayedinthiswindowTheRotationandMirroritemscontroltheorientation oftheimageinthewindowTheNoOverlayitemallowsyoutoturnoallcoloroverlay itemsiecrosshairsanatomicalmarkersandfunctionTheMintoMaxandto%

MCWAFNI2.00 { Dec6

itemschoosehowthevaluesintheimagearrayaremappedtograyscalelevelsonthescreen. Theformerchoicemapstheminimumimagevaluetoblackandthemaximumtowhite� thelatterchoicecomputesthecumulativehistogramoftheimageandmapsthepoint toblackandthepointtowhite.

TheFreeAspectcontrolletsyouresizetheimagewindowtoanybizarreaspectratio. Normallytheprogramrestrictstheimagewindowresizingsoastokeepthedatavoxelto displaypixelgeometricrelationshipcorrectassumingthatdisplaypixelsaresquare.

TheSavecontrolsactuallyhavenothingtodowithimagedisplayTheyarejusthere becauseitwasaconvenientplacetoputthemTheycontroltheoperationoftheSave: buttonontheimageviewingwindownexttotheDispbuttonthisisdiscussedbelow.

TheTranmenusallowyoutopickfromalistofimagetransformationsTheTranD transformationsareallpointwisethatistheimageintensityoutputatagivenpixelis afunctionoftheimageintensityinputatthatgivenpixelonlyThebuiltinTranD functionsareLogandSSqrtwhichtakethecommonlogarithmlogofeachpixel, andtakethesignedsquarerootsgnxjxjofeachpixelrespectively.

TranDfunctionsaremoreglobalimagetransformationswheretheimageintensity outputatagivenpixelcanbeafunctionofotherpixelsTheonlybuiltinTranDfunction isMedianwhichreplaceseachpixelbythemedianoversitsneighborhood.

AFNIpluginauthorscanaddfunctionstotheseTranmenushopefullytheywillbedocumentedAtthebottomoftheDisppanelareotherbuiltinimageprocessingfunctions:

FlattenHistogramatteningorequalizationisperformedontheimagepriorto display.

SharpenHighemphasissharpeningisperformedontheimagepriortodisplayWhen printingimagesonprinterswithrelativelyfewcolorsavailableperpixelthecombinationofMedianandSharpengivesniceresults.

EdgeDetectSobeledgedetectionisperformedontheimagepriortodisplay.

Ifmorethanoneoftheseareselectedtheyareperformedinthetoptobottomorderas displayedalsotheseoperationsareperformedafteranyTranfunctions.

SaveControl

ThisbuttontakesoneofthreeformsdependingonthechoicesmadeintheDisppanel:

SaveoneThisformoftheSavefunctionisselectedbytogglingontheSaveOneoption ontheDispcontrolpanelInthisformtheactionistosavethecurrentimageto diskThisistheonlywayprovidedbyAFNItosaveamontagelayout.

Thisbuttonpopsupalittlechooserwindowwhichasksyoutoinputthelename

prexfortheoutputimageTheimagewillbesavedintherawPNMformatwiththe

nameprefixpnmImagesinthisformatcanbeconvertedtootherformatssuchas ! TIFFwithcommandlineutilitiesinthenetpbmpackageorthexvsharewareprogram. ^{netpb^m}ImageswhichcontainnocolorwillbesavedinthePGMformatimageswithcolored

andxv

pixelswillbesavedinthePPMformat)

SavepnmThisformoftheSavefunctionisselectedbytogglingonthePNMSaveoption ontheDispcontrolpanelInthisformtheactionistosaveacollectionofsliceimages underlayandcoloroverlaytodiskintherawPNMformatEvenifamontageis beingdisplayedonlysinglesliceswillbesavedwiththisfunction.

Thisbuttonalsopopsupachooserwindowwhichasksyoutoinputthelename prexfortheslicedataIfyouenterfredfortheprexthenthe^thslicewouldbe namedfredpnmAfteryoutypeinthedesiredprexyouclicktheSetbutton, andthenmustchoosetherstandlastsliceindexesforthesaveoperationfromthe newchoosersthatwillpopupWhenyouSetthelastsliceindexthewritetodisk operationstarts.

SavebkgThisformoftheSavefunctionisselectedbytogglingothePNMSaveand SaveOneoptionsontheDispcontrolpanelInthisformtheactionistosavethe backgroundimagepixelvaluesThisdoesnotmeanthegrayscaleintensitiesdisplayed inthewindowItmeansthattheactualvaluesstoredinthedatasetBRIKlewillbe writtentodisk.

ThisbuttonoperatessimilarlytotheSavepnmfunctionyoumustchoosealename prexandtherstandlastsliceindexesforthesaveoperationIfNsizeSaveis selectedontheDispcontrolpanelthenthesavedimageswillbeexpandedtothe nextlargestpoweroftwo.

UsingtheFunctioncontrolsyoucanswitchtohavethefunctiondisplayedasthe backgroundInthatwaythefunctionaldatasetvoxelvaluesmaybewrittentodisk insliceformatAlternativelytheauxiliaryprogramfromdcanbeusedtowriteslice imagelesoutofadataset.

ForallSaveoptionstheactualsizeofthedisplayedwindowdoesntmattertheimages savedtodiskwillreectthevoxeldimensionsofthedatasetInparticularifthedataset voxelsarenotsquareintheplaneofviewthenthesavedimageaspectratiowillbedistorted. TheonlywaytorectifythisinAFNIistoswitchthedatasettobewarpondemandusing theDatamodecontrolswhichalwaysinterpolatestosquarepixels.

Toactuallysavethepixelsasdisplayedonthescreensomesortofsnapshotorwindow grabutilityisneededIfnoneotherisavailablethesharewareprogramxvhasawindow grabfunctionOrthexwdcommandlineprogramcanbeusedwithappropriateconversion usingthenetpbmutilitiesForexampletheimagesdisplayedinthismanualwerecaptured withvariantsofthefollowingcommandline:

xwdframexwdtopnmpnmdepthppmtopgmpgmnormpnmtopsnoturnnameeps

Montcontrol

ThisbuttonallowsyoutomakeamontageofmorethanonesliceintheimagewindowIt popsupacontrolpanelpicturedearlierandbelowForconvenienceinprogrammingonly oneoftheDispandMontcontrolpanelscanbeopenatatimeperimageviewerThis restrictionmaybeliftedinsomelaterversionofAFNIbutnoguarantees.

ExampleofslicemontagewithMontcontrolpanel

Thevemontagemenucontrolsfromtoptobottomare:

AcrossThiscontrolsthenumberofslicestobedisplayedhorizontallyacrossthewindowIntheexampleaboveAcrossandDownarebothsetto.

DownThiscontrolsthenumberofslicestobedisplayedverticallydownthewindow.

SpacingThiscontrolsthefrequencywithwhichslicesaredisplayedSpacingof1 meansthatadjacentsliceswillbedisplayedmeansthateveryotherslicewillbe displayedetcTheunitsofthisselectorareslicesnotmillimetersthuschanging theresolutionofawarpondemanddatasetusingDatamodecontrolswillchangethe interslicedistanceasdisplayedhereIntheexampleabovetheimagesareslices apartSincethisisintheTalairachviewwhichcanbeseenfromthedatasetnamesin theimageviewertitlebarandthedefaultvoxelsizeofmmwasusedthesesagittal slicesaremmapartcentertocenter.

BorderThiscontrolsthethicknessindatasetpixelsnotscreenpixelsoftheborder todrawbetweensliceimagesIntheaboveexamplethisissetto.

ColorThiscontrolsthecoloroftheborderdrawnbetweensliceimagesIntheabove examplethisissettoagraycolorunderthepresumptionthatyoudonothavea colorPostScriptprinterwithwhichtooutputthismanual.

AcrossthebottomoftheMontcontrolpanelarefouractionbuttonsTheirfunctionsare:

QuitThiswillclosetheMontcontrolpanelandleavethecurrentmontagelayout unchanged.

xThiswillresettheAcrossandDowncontrolstoeachbeThisissimplya convenienceforwhenyouwishtogobacktodisplayingasingleslice.

DrawThiswillinstructtheimageviewingwindowtoredrawitselfascurrentlycommandedThisbuttonwilldisplayininvertedcolorsuntiltheredrawoperationis completeIfthedatasetiswarpondemandandmanyslicesarerequestedthis operationmaytakeseveralseconds)

SetThiscombinesthefunctionsofDrawandQuititwillredrawthewindowas commandedandalsoclosetheMontcontrolpanel.

SlicesaredisplayedstartingintheupperleftcornerthenfromlefttorightthentoptobottomIftheDispcontrolsareusedtorotateormirrortheimagestheseoperationsapply toeachsliceindividuallynottothemontageasawhole.

IfthenumberofslicesdisplayedAcrossDownislargeandSpacingislargethenthe extremeslicesrequestedmaybeoutsidethedatasetInsuchacasethetoggleWrapon theAFNIcontrollerwindownexttotheGapmenucontrolswhathappensIfWrapis turnedonthenslicesrequestedpasttheedgeofthedatasetwillbewrappedbacktothe oppositeedgeIfWrapisturnedothenslicesrequestedpasttheedgeofthedataset willbelledwithzeros.

Theonlysliceimagewhichwillhavecrosshairsdisplayedistheonecontainingthecurrent viewpointClickingmouseButtoninanysliceimagewillcausethecurrentviewpointto jumptothatlocationinthatsliceThiswillalsocausethatslicetojumptothecenter positioninthemontagelayout.

IftheXhairsbuttonissettoMultithenorthogonalimageviewingwindowswillshow crosshairsforeachslicedrawninthemontagedwindow.

TheonlywaythatAFNIprovidestosaveamontagedisplaytodiskistheSaveone functiondescribedearlierThisfunctionasallSavefunctionssavestheimageatits naturalsizeoneoutputpixelperdatasetpixelregardlessofanywindowresizingyou mayhaveimposed.

PopupMenu

IfyouclickandholdmouseButtonusuallytherightmostbuttonwhilethecursorisinan imagewindowamenuwillpopupatthatpointTherstitemonthemenuisJumpback. ThiswillresetthecrosshairviewpointtothelastlocationclickeduponThemainuseof thisfeatureistorecoverfromaccidentallyclickingButtoninaninconvenientlocation.

TheseconditemonthepopupmenuisJumptoThiswillpopupawindowinwhich youmayenterthexyzcoordinatesDICOMorderofthepointtowhichyouwishto setthecrosshairviewpointOneapplicationtheclusterlocationsreportedbydclustmay bepastedintothewindow)

ThethirditemonthepopupmenuisImagedisplayThiswillcollapsetheviewing

windowtojustincludetheimageSelectingthisitemagainwillbringtheviewingwindow

controlsbackOneapplicationmakingsnapshotsofnicefunctionaldisplaysNBThis

functiondoesnotworkwellonallXdisplaysforunknownreasonsItmaycollapsethe

imagewindowtozerosizewhichisslightlyinconvenient. ! WhenallthreeviewingwindowsAxialSagittalandCoronalareopenthebottom ^Seeingitemonthepopupmenuwillcontainadisplayofthebackgroundpixelvalueatthecenterof

individual voxel values

thecrosshairsThebackgroundisnormallyananatomicalimagebutcanalsobeswitched tobeafunctionalimageusingtheFunctioncontrols)

ResizingImageWindows

Whenaviewingwindowisrstopeneditisatthenaturaldimensionfortheresolutionset intheDatamodecontrolsorinthedatasetheaderleifviewingfromthedatabrickWhen jumpingfromonecoordinatesystemtoanotherorfromonedatasettoanothertheprogram attemptstokeeptheonscreenpixelsmmthesamesothatnosuddenscalechangesoccur.

Whentheviewingwindowsareresizedtheimagesarestretchedbynearestneighbor resamplingThishasnothingtodowiththeresamplingmodessetintheDatamodeand FunctioncontrolsForexamplethecrosshairsareexactlyonepixelthickinthenatural' dimensionofeachwindowIfawindowisstretchedthenthecrosshairswillbecomethicker. Ifawindowisshrunkthecrosshairsmaydisappearwhentheyaremissedduringthe displayresampling.

Whenviewingfromthedatabrickandwhenthedatavoxelsarenotcubicaltheviewing windowswillsimilarlystretchthecoarserdirectiontomaintainthecorrectphysicalaspect ratioonthescreenassumingthattheXpixelsaresquareThiscanproduceablocky lookingimageToforceasmoothingtheWarponDemandmodeshouldbeused.

SampleGraphingWindow

GraphDisplay

WhenthecurrentanatomicaldatasetisDtimeandisnotsettowarpondemandusing theDatamodecontrolsthenthethreeGraphbuttonsnexttotheImagebuttonswillbe activatedTheseallowthedisplayofgraphsofvoxelintensityvstimeAlthoughAFNI

MCWAFNI2.00 { Dec6

graphwindowslookverylikethegraphwindowintheauxiliaryprogramFDthereisat ! leastonemajordierenceAFNIgraphwindowscanberesized)

TheabovegureshowsasamplewithdatatimeseriessubgraphsdisplayedThe

centralsubgraphisborderedinalightcolorhereashadeofgrayThissubgraphisa

plotofthedatatimeseriesattheviewpointvoxeltheonedisplayedatthecrosshairsin

theimageviewingwindowsTheothersubgraphsareofneighboringpixelsinthiscasein

thesagittalplaneInthecorrespondingsagittalviewingwindowthecrosshairswillshow

aboxoutliningthepixelsbeinggraphedIfyoushifttheviewpointinanimageviewer,

thenthegraphviewpointwillshiftaccordingly.

Thevoxelindexesoftheviewpointareshownatthelowerleftedgeofthegraphdisplay�

forexampleZmeansthatthisisslicenumbercountingfromThenthespacing

betweenverticalgridlinesintimestepsisshowninthiscasethereisagridlineevery^{t^h}

timestepTheNumlabelshowsthenumberofpointsinthetimeseriesAtthebottomof

thegraphsisalabelstartingwithindexThisshowsthetimeindexofthecurrentpoint

whichcanbealteredwiththeIndexcontrolontheAFNIcontrollerwindowthevalue

ofthetimeseriesatthatpointandthetimecoordinateofthattimeindexinthiscase,

secondsThecurrenttimepointisdisplayedwithalittleredballoverlaidnthe

centralsubgraphinthegureaboveredisrenderedingray. ! Attheleftofthegraphsaretwonumericlabelsinthiscaseand. ^GraphThisshowstheverticalrangeofthecentralsubgraphInthisdisplayeachsubgraph

scaling

hasitsminimumpointatthebottomofitssubwindowEverysubgraphhasthesame verticalscalefactorbuthasadierentverticalosetThisissothattheywillalltinthe samedisplayeasilyThiscanbeconfusingwhencomparinglevelsofadjacentpixelsitis importanttorealizethattherecanbeanarbitraryconstantosetbetweenadjacentsubgraphsTheBaselinebuttonontheOptmenucanbeusedtoensurethatallsubgraphs areplottedwiththesameverticaloset.

ButtonClicksinaGraph

Atthelowerleftofthegraphwindowisalogowhosemainfunctionistoremindyoufrom whichplanethesegraphsaredrawnThiscanbesuppressedforwindowsnapshotpurposes) byclickingButtononthelogoClickingButtoninthatspaceagainwillrestorethelogo. TheFIMandOptbuttonswillalsobehiddenandrestoredbytheseoperations)

ClickingButtononthecentralsubgraphwillcausethetimeindextojumptothat pointIftheShiftorCtrlkeyispressedwhiledoingthisthetimeindexinsteadwill moveupordownbyinwhicheverdirectioncorrespondstothemousecursorrelativeto thetimeindexindicatorball.

ClickingButtononanyothersubgraphwillcausethespatialviewpointtojumptothat locationwithoutchangingthetimeindexClickingButtononasubgraphwillpopupa smallwindowwithsomestatisticsaboutthattimeseries.

Somekeystrokesifpressedwhilethegraphwindowhasfocuswillcarryoutcertain functionsThesefunctionsarealsoavailablefromtheOptmenuandaredescribedbelow.

MCWAFNI2.00 { Dec6

GraphingFIMleftandOptrightmenus

Optmenu

Theitemsonthismenucontroltheappearanceofthegraphs:

ScaleThisisapullrightmenuusedtocontroltheverticalscaleofthegraphsThe gureaboveshowsthesubmenuthatresultsfrompullingrightonthisitemThe DownandUpbuttonswillcausethegraphstoscaledownshrinkandupgrow. PressingthekeysandinthegraphwindowwillhavethesameeectsThe Choosebuttonwillcausealittlechoosertopopupwhichallowsyousetthevertical scalefactormanuallyIfthescalefactorispositivethenitisthenumberofscreen pixelstouseperunitofdataIfthescalefactorisnegativeitsabsolutevalueisthe numberofunitsofdataperscreenpixelThusincreasingthescalefactorwillcause thegraphtogrowverticallyThereisnoprovisioninAFNIforautomaticscalingto tthedatasetrangeeachgraphwindowstartswithitsscalefactorsettoJudicious useoftheorkeysmaybeneededtomakeagraphvisible.

MatrixThispullrightmenuisusedtocontrolthenumberofsubgraphsdisplayedIt showsasubmenusimilartotheScalesubmenuInthiscaseDownkeystrokem) willcausethenumberofsubgraphsdisplayedacrossanddowntodecreasebyUp keystrokeMwillincreasethearraysizebyChoosewillletyoudirectlysetthe numberofsubgraphs.

GridThispullrightmenuletsyoucontrolthespacingintimestepsbetweenvertical gridlines.

SliceThispullrightmenuletsyoumovethespatialviewpointbetweenslicesinthe datasetmovingwithinasliceiscontrolledbyButtonclicksasdescribedabove.

GridColorThisitemjustrotatestheverticalgridcolorbetweentheavailablechoices.

MCWAFNI2.00 { Dec6

BaselineThisitemswitchesthewaythatgraphbaselinesarecomputedBydefault, eachsubgraphhastheminimumvalueofitstimeseriesmappedtothebottomof itssubwindowBypressingthisitemorthebkeythesubgraphswillswitchto havingacommonbaselineThatistheminimumvalueinallthedisplayedtime serieswillmappedtothebottomofeachsubwindowInmanycasesdoingthiswill requirescalingdownthegraphswiththekeyChoosingthisitemagainwillrestore theoriginalgraphbaselinemode.

WriteCenterSelectingthisitemorpressingthewkeywillwritethedatasettime seriesinthecentralsubgraphtodiskinalenamelikesuffixDThe suffixisselectedbythenextmenuitemSetwSuffixandtheprexnumbers arefromthevoxelspatialindexinthedatasetTheoutputleisASCIIonenumber perlineNBtheoutputisthedatasettimeseriesandisunaectedbytheTran transformationsbelow)

TranDThisitemisthesameastheTranDitemontheimageviewerDisppanelIt allowstheapplicationofapointwisetransformationfunctiontothetimeseriesbefore graphingoccurs.

TranDThisitemallowstheapplicationofgeneraltransformationstothetimeseries beforegraphingThetwobuiltinTranDfunctionsareMedianandOSfilt, whichareorderstatisticssmoothingltersusingawideneighborhoodInaddition, thepluglsqfitplugindenestwomorefunctionswhichcanbeusedtodolinear leastsquarestsofvariousfunctionstodatasettimeseries)

DoublePlotNormallyifaTranDtransformationisappliedthegraphofthetransformeddatareplacesthegraphoftheoriginaldataIfthisitemisselectedthenboth graphswillbedisplayedThiswasaddedtobeabletoseetheleastsquarestsfrom pluglsqfitplottedovertheinputdata)

DoneThisclosesthegraphingwindowthekeystrokeqhasthesameeect.

FIMmenu

Thismenuisusedtocontrolthecomputationoffunctionaldatasetsoftheficotypefrom DtimedatasetsSomeofthefunctionsofthismenuareduplicatedontheFunction controlpanelFIMmenu.

TheoryofFIM

Ifxnisadatatimeseriesandrnisaknownreferenceoridealvectorcorrespondingtothe expectedactivationtimecoursethenthestatisticalmodelforxnis

xnrabnn n) nNiid.

whereistheunknownamplitudeoftheactivationaistheunknownmeansignallevel, bistheunknownlineardriftintimeandistheunknownnoisevarianceThecorrelation

MCWAFNI2.00 { Dec6

methodcomputesthesamplecorrelationcoecientbetweenxnandrnandusesthat todeterminethesignicanceofthehypothesisthat

TimeSeriesFiles

MCWAFNIstoressingletimeseriessuchasrnintheformatdescribedearlierASCII formatonenumberperlineAnumbergreaterthanmeansthatparticularpoint intimeshouldbeignoredThisconventiongoesbacktotheoriginalmprogramin, andisduetoAndrzejJesmanowiczofMCWTheWriteCenterbuttondescribedabove isonewaytocreatesuchatimeseriesleAnotheriswiththeauxiliaryprogramsqwave. Yetanotherissimplytouseatexteditorsuchasvi)

WhenAFNIstartsupitwillreadintimeserieslesfromthesessiondirectoriesthat itopensTheprogramwillattempttoreadatimeseriesfromanylewhosenameends inDThesetimeserieswillbepooledintoalibrarywhoseentriescanbeselected fromamenuasdescribedbelow.

Youmaywishtokeepsometimeserieslesstoredseparatelyfromanyparticularsession directoryAFNIcanbemadetoreadsuchlesbydeningtheshellenvironmentvariable AFNITSPATHLiketheexecutablesvariablePATHthisisacolonseparatedlistofdirectories inwhichtosearchforparticularlesinthiscaseDlesForexample:

setenvAFNITSPATHfHOMEgtimeseries/

willcauseAFNItosearchfortimeseriesinthetimeseriesdirectoryunderyourhome directoryandinthecurrentworkingdirectoryNormallyyouwouldputthistypeof commandinyourcshrclesothatitwouldalwaysbeexecutedwhenyouloginIm assumingthatyouusetheCshellcshoritssupersettcsh)

IsaidabovethattimeserieslesarestoredasonenumberperlineThisistrueofthe olderprogramssuchasmFDetcbutAFNIitselfallowsmorethanonenumberper lineInthiswaymorethanonetimeseriescanbestoredperle:

.	.	.	.
			9
			9
0	0	0	0
0	0	0	0
0	0	0	0
0	0	0	0
0	0	0	0
0	0	0	0
0	0	0	0

TheaboveexampledenesfourtimeseriesinoneleEachonestartswithtwos, whichindicatesthatthesetwopointsshouldnotbeusedinanyanalysiswiththesetime seriesThesubsequentvaluescouldbeusedasanidealwaveforminFIManalysisInthis exampleeachtimeseriesaftertherstisatimedelayedcopyoftheonetotheleftAUnix commandoftheform

prmtsaDbDcDdDabcdDx

canbeusedtogluemultiplelestogetherhorizontallyintoasinglelewithmultiple columnsYoushouldbesurethatalltheleshavethesamenumberoflinesbeforeusing theprcommandwhichisreallyaprogramdesignedforformattinglesforprintoutOn SGIworkstationstheprcommandhasasmallupperlimittothenumberofcolumnsitwill outputOnsuchsystemsitmaybenecessarytopasteupalargenumberofcolumns intwostages)

Toallowsuchtimeserieslestobedistinguishedfromordinarylescontainingonly onetimeseriesAFNIallowstheuseofthelenamesuxDxasintheprcommand exampleaboveHoweverthereisnodierencebetweentheDxlesandtheDles asfarasAFNIisconcerneditisperfectlyacceptabletohaveamulticolumntimeseries lenameendinDortohaveasinglecolumntimeserieslenameendinDx.

AtthisreleaseonlytheactualAFNIprogramwillrecognizethesemulticolumntime serieslescorrectlyOtherprogramssuchasmstillrequireeachletocontainonly onetimeseries.

Sampletimeserieschoosermenu

FIMMenuItems

PickIdealThisbuttonpopsupachooserwindowwhichallowsyoutoselectatime seriesletobeusedastheidealwaveformrnanexampleofthischooserisshown aboveWitheachtimeserieslenameisshownthedimensionsofthetimeseries. IntheexampletheleqqqDxhaspointsintimelinesofdataandhas3 columns.

IftheidealtimeserieshasmorethanonecolumntheFIMcomputationscomputethe correlationcoecientofeachvoxelwitheachcolumnseparatelyThenthecolumn thatismosthighlycorrelatedwiththevoxeltimeseriesisselectedtocomputethe� forthatvoxelbecomestheintensityandthecorrelationcoecientbecomesthe secondsubbrickstoredintheresultingficodataset.

WhentheidealtimeseriesisselecteditwillbeplottedatthetopofthecentersubgraphwindowinredSectionsofitthataremarkedtobeignoredwillbeplottedin blueIfthereismorethanonecolumnintheidealtimeseriesbydefaulttheywillall beplotted.

BythewaythePlotbuttononthetimeserieschooserispermanentlydeactivated. Iintendedtoprovidetheabilitytopreviewatimeseriesinalittlewindowbutnever gotaroundtoimplementingitThebuttonremainstoremindmeofthisandto remindmeofallmyothergoalsforAFNIthathaveyettocometofruition)

PickOrtInthemathematicalmodelforxngivenearliernotethatweincludedabnin themodeltorepresenttheunknownbaselineanddriftofthedatatimeseriesThese areortstimeseriestowhichthedatatimeseriesisorthogonalizedpriortothe correlationcoecientcalculationAFNIalwaysorthogonalizesthedatatothese twotimeseriesInadditionyoumayspecifyanothertimeseriestowhichthedata timeseriesineachvoxelshouldbeorthogonalizedIftheorttimeserieshasmorethan onecolumneachdatatimeserieswillbeorthogonalizedtoallcolumnspriortothe correlationcoecientcalculation.

WhentheorttimeseriesisselecteditwillbeplottedinthemiddleofthecentersubgraphwindowingreenSectionsofitthataremarkedtobeignoredwillbeplotted inblue.

EditIdealThispullrightsubmenushowninagurefaraboveisusedtocontrolthe idealwaveformThemenusubitemsare:

IdealCenterwilltakethecentralsubgraphdatatimeseriesandmakeitthe idealtimeseries.

IdealCenterwilltakethecentralsubgraphdatatimeseriesandaverageit intotheidealtimeseriesInthiswayitispossibletoselectagroupofvoxels oneatatimeandaveragethemtogethertomakeasinglewaveform.

SmoothIdealwillapplyaneighborhoodorderstatisticsltertosmooththe currentidealwaveformIfthepointsinputareabandcthentheoutputis

ynmedianabcmaxabcminabc:

ShiftIdealwillpopupacontrolpanelthatallowsyoutogenerateshiftedcopies ofthecurrentidealwaveformAlltheshiftedcopiesformamulticolumntime seriesInthiswayitispossibletoconstructasinglecolumnidealwaveformuse AFNItocreatetimeshiftedcopiesofitandthencorrelatethemallwiththe datapickingoutthebesttimeshiftateachvoxel.

ClearIdealwillclearthecurrentidealwaveformthatistheidealwaveform willbeundenedafterthisispressedThegraphoftheidealwaveformwillalso becleared.

ClearOrtwillclearthecurrentortwaveform.

ReadIdealallowsyoutoreadintheidealwaveformfromanexternalle.

WriteIdealallowsyoutowritethecurrentidealwaveformtodiskInthisway, anidealcreatedfromthecurrentdatasetcanbesavedforlateranalysis.

StoreIdealallowsyoutostorethecurrentidealwaveformintotheAFNImenu forpossiblelaterselectionTheonlywaytocreateanortfromadatasetisto rstcreateitasanidealthentostoreitwiththisbuttonandthentouse

PickOrttogetitothetimeseriesmenuTheWriteandStoreoperations areindependentwritingtodiskdoesnotimplystoringinthemenusystemor viceversa.

IgnoreThispullrightmenuallowsyousetthenumberofpointstobeignoredatthe beginningofeachtimeseriesThisisoftendesirablesinceinrapidscanMRIthe longitudinalmagnetizationmaytakeseveralimagestoreachsteadystateTimepoints thatareignoredeitherthroughtheuseofthiscontrolorlargevaluesinthe idealwaveformwillbeskippedinthecorrelationanalysisInadditionpointsthat areignoredwiththiscontrolwillnotbegraphedThisallowslargeinitialtransients tobesuppressedandmakesiteasiertoreadthegraphs.

FIMPlotsThispullrightmenuallowsyoutospecifywhetherallthecolumnsoftheideal andortwaveformsshouldbeplottedorjusttherstcolumns.

ComputeFIMThiswillstartthecorrelationcalculationsAttheleastanidealwaveform mustbespeciedbeforethisbuttonwillworkYoumayalsowishtosettheIgnore valueandtheortwaveformpriortothesecomputations.

ThecalculationsusetherecursivemethodofCoxetalWhiletheyareproceeding, aprogressmeterwilldisplayoverthetitlebaroftheAFNIcontrollerwindowWhen theresultsarenishedthenewficodatasetwillbecomethecurrentfunctional datasetandcanbeexaminedimmediatelyintheimageviewersIftheinputDtime datasetwerenamedelvisorigthentheficodatasetwillbenamedelvisorig, wherewillbeoneofIfdesiredtheDatasetRenameplugrenamec) plugincanbeusedtochangetheprextosomethingmoreconvenient.

ViewingControls

ThesecondcolumnoftheAFNIcontrolwindowcontainsmanycontrolsthataecthowthe datasetsareviewedtransformedandoutput.

ViewModes

AtthetopofthissecondcolumnaretheviewmodecontrolsTheseletyouswitchbetween theavailableviewsOriginalACPCalignedorTalairachIfaparticularviewisnot availableforthecurrentlyactiveanatomicaldatasetthenthecorrespondingbuttonwill beinactivegrayedout.

WhenyouswitchviewmodesyouwillseethatthewindowschangesizeThatisbecause intheacpcandtlrcviewstheimagesareclippedtotheknowndimensionsofhuman

MCWAFNI2.00 { Dec6

headsThisistosavespacewhensuchdatasetsarewrittentodiskThewindowresizing issetuptopreservethepixelsperbrainmillimeterratioTheprogramalsoattemptsto keepthecrosshairviewpointinthesameanatomicallocationastheywereintheprevious viewmodebuttheymayshiftslightlySincetheorigviewwillgenerallyberotatedfrom theacpcandtlrcviewskeepingtheviewpointatthesamelocationdoesnotmean keepingtheslicesinthesamelocation.

DefineControls

EachDefinebuttonopensupanothercontrolpaneltotherightofthissecondcolumn. TheyarediscussedseparatelylaterNotethattocloseaDefinecontrolpanelyoupressits buttonagainTohelpwiththistheDefinebuttonsthatarecurrentlyopenaredisplayed ininvertedcolorsYoumayopenmorethanoneDefinecontrolpanelatatimebutthey willalllieontopofeachothermostrecentlyopenedpanelontop.

SwitchControls

Thesecontrolsletyouchoosewhichsessionandwhichdatasetsfromthatsessionyouare viewingatanygivenmomentTheypopupachooserthatletsyoucyclebetweenthesession directoriestheanatomicaldatasetprexesandthefunctionaldatasetprexesrespectively.

WhenyouswitchdatasetsAFNImaybeforcedtoswitchviewsaswellThiscanoccurif thenewdatasetdoesntexistintheviewmodeyouwereformerlyinForexampleifyousave severalfunctionaldatasetsintheTalairachviewmodeusingtheDatamodecontrolsthen combinethemwithdmergetheresultwillonlyexistinthetlrcviewYoucanonlyview thisfunctionaldatasetwhentheviewmodecorrespondssotheprogramwilljumptothat modeIfsuchaviewmodeswitchoccurstheprogramwillbeepwhenitmakesthetransition.

DefineMarkers

ThetransformationtotheACPCalignedviewandfromtheretotheTalairachviewis accomplishedbymeansofmarkersTheseareanatomicallandmarksthatyoumanually selectusingthecontrolcolumnopenedupbythiscontrol.

OnlyDanatomicaldatasetscanhavemarkerssetDtimedatasetshavethemarkers disabledItisonlypossibletotransformaDtimedatasettoTalairachcoordinatesusing aparentDdatasetasdescribedearliertheXsandOsdiagram.

MarkersfortheACPCAlignedTransformation

TheACPCalignedviewmodeisdenedbyarigidbodytransformationthatmakesthe ACPClinethenewyaxismakesthelongitudinalssurethenewxzplaneandmakes thelineperpendiculartothatthenewxaxisrighttoleftTheneworiginisputatthe intersectionoftheACPClineandtheverticallinepassingthroughtheposteriormargin oftheACSeefordetails.

Cartoonofcentralbrainshowingkeyanatomicallocations

ToselectthelandmarksyoumustrstchooseAlloweditssothatAFNIwillletyou changethemarkersAfterthatyouchoosethevelandmarks:

ACsuperioredgeThehighestpointontheanteriorcommissureinthemidsagittal plane.

ACposteriormarginTherearmostpointontheanteriorcommissureinthemidsagittalplane.

PCinferioredgeThelowestpointontheposteriorcommissureinthemidsagittal plane.

FirstmidsagptTwopointsarerequiredinthelongitudinalssuretheyareused todenethenewzaxisTwopointsarerequiredtomakesurethatthenewvertical planeisdenedadequatelythemismatchbetweentheACPClineandthesetwo pointsmustbelessthan^�)

AnothermidsagptShouldbeatleastmmawayfromtherstone.

OriginalleftandACPCAlignedrightDefineMarkersControlPanels

Youselectalandmarkbydepressingitsbuttonthenmovingthecrosshairstothedesired locationthenclickingtheSetbuttonAvisiblemarkerwillappearYoucanresetthis pointorClearitWhenamarkerissetitstogglebuttonwillappearininvertedcolors.

TheatlasdenitionsofthemarkerlocationsarealwaysintermsofaboundaryThat

isslightlyambiguouswhenitcomestodiscreteimagesdoyoumarkthelastvoxelvisible

inthestructureortherstvoxeljustoutsidethestructureMyarbitrarysolutiontothis

problemisalwaystomarkthelastvoxelvisibleinthestructureForexampleinmarking

thetopoftheACImoveupuntilitisjustnolongervisibleintheaxialimageThen ! IdropbackdownoneaxialsliceItispossibletousewarpondemandtoplacemarkers

Subvoxel

atsubvoxellocationsseetheDatamodecontrols.

marker locations OnMRimageswithmmvoxelsandwithgoodgraywhitemattercontrastitisusually

quiteeasytosettheACmarkersAtMCWweuseaGESignaSPGRsequenceforthis

purposeThePCishardertospotbutitisalwaysnearthetopofthecerebralaqueduct

insubjectswithnormalanatomyitmightbedisplacedbysomepathologicalconditions�

ifyoususpectthishashappenedconsultaneuroradiologistimmediatelyExamination

ofthesampleAFNIdatasetandsomeconsultationwithaneuroanatomytextbookwill

probablybehelpfulinlearningtorecognizetherequiredanatomicallandmarks.

MakingtheTransformation

WhenallmarkersaresettheQualitybuttonwillbecomeactiveThisbuttonwillcheck themarkersetforelementaryconsistencyIfthemarkersdontpassthetestanerrormessage popsuptoexplainwhathappenedIftheydopassthetestthentheTransformData buttonbecomesactiveWhenyoupressthisthenewdatasetwillbecreatedinthiscase, theacpcviewoftheanatomicaldatasetyouwerejustmarkering.

ThisnewdatasetwillnothaveaBRIKleondiskjustaHEADleWhenAFNIcomes todisplaythisdatasetitwillsimplytransformtheneededdatafromtheorigdataset. IfyouwishyoumaysavethedatavoxelsinthenewviewtodiskusingtheDatamode controlsIfyouwishtomanipulateatransformeddatasetusingtheauxiliaryprograms, youwillhavetosavethedatavoxelstodisk)

TransformationtoStereotaxicieTalairachCoordinates

AfteryoucreatetheACPCalignedviewyoucanswitchtoitwiththeACPCAligned buttonAtthispointyoucansetmarkersforthescalingtotheTalairachviewSixmarkers arerequiredtodenetheboundingboxofthecerebralcortexTheseshouldbesetquite carefullysinceitisofteneasytomistakethesagittalsinusforcortexwhichwouldgivean erroneouslylargeboxinthezdirectionGenerallyIndthatthemostinferiorpointin oneofthetemporallobesisthehardesttopickout.

Intheacpctlrctransformationmarkercontrolpanelatoggleswitchlabeled BigTalairachBoxappearsjustbelowtheTransformDatabuttonIntheearliestversionsofAFNIthebraindatawasclippedatmminferiortotheACPClinethisbeing thelocationofthebottomoftheTalairachTournouxatlasguresInsubsequentworkwe foundthiswasinadequateforcerebellarimagingThenewdefaultclippinglevelismm

MCWAFNI2.00 { Dec6

inferiortotheACPClineandthisisreferredtoastheBigTalairachBoxDatasets BRIKscreatedwiththeoldsmallboxsizearesmallerthanthenewboxsizeThereisno waytomixoldandnewboxsizedatasetstogetherwhenusingtheauxiliaryanalysisprograms suchasdANOVAForthisreasonandtomaintaincompatibilitywitholdanalysesitis possibletowriteoutoldboxsizedatasetBRIKsbytogglingthisswitchoForallfuture workIstronglyrecommendusingthenewTalairachboxsize.

ThetransformationcarriedoutispreciselytheonedescribedinandIrecommend thatanyoneusingAFNIreadthisatlasThedatasetisdividedintosubvolumes:

InxRighttoMidsagittalMidsagittaltoLeft

InyAnteriortoACACtoPCPCtoPosterior

InzInferiortoACACtoSuperior

Eachregionisscaledseparatelytomatchthemillimetriccoordinatesintheatlas:

xaxisACPClinetomostleftpointofcerebrummm

xaxisACPClinetomostrightpointofcerebrummm

yaxisMostanteriorpointofcerebrumtoACmm

yaxisACtoPCmm

yaxisPCtomostposteriorpointofcerebrummm

zaxisMostinferiorpointofcerebrumtoACPClinemm

zaxisACPClinetomostsuperiorpointofcerebrummm Theatlasbrainisfromanadultfemaleandsoatypicaladultmalebrainwillbeslightly compressedbythesestandardmeasurementsAnyjokesatthispointwillbesternlydealt withThistransformationisthencombinedwiththeorigacpctransformationso thatthedataviewedintheTalairachmodeisonlyinterpolatedoncenottwice.

Thewholeproceduretoproducethetlrcviewfromtheorigviewonlytakesafew momentsonceyoubecomeadeptatrecognizingtherequisiteanatomicallandmarks.

Youwillndthatthemarkertogglebuttonsandsetclearbuttonsareduplicatedonthe popupmenufromtheimagingwindowsThisisforconveniencesinceitisoftennecessary topeercloselyatthescreentodecideonamarkerpointandIpersonallynditannoyingto havetoswitchmyattentiontoanotherwindowinordertosetthemarkerAlsonotethat depressingthetogglebuttoninthemarkercontrolcolumnoronthepopupmenuforan alreadysetmarkerwillcauseAFNItojumpthecrosshairviewpointtothatmarkerlocation.

FinallynotethattherearenomarkersavailabletobesetintheTalairachviewmode. Atpresenttherearenotransformationsbeyondthisonemaybesomeday.

RetransformationandRecreationofDatasets

Ifyoudecidetoremarkandretransformananatomicaldatasetthentheoldtransformed versionwillbedeletedfromdiskbeforethenewversionismadeNotonlythatbutall theautomaticallymanufacturedtransformeddatasetsthatfollowonthistransformation willalsobedestroyedandremadeThiscanbedisconcertingatrstbutitistheonly logicalcourseofactionforAFNItotakeotherwisethetransformedfunctionaldatasets

MCWAFNI2.00 { Dec6

wouldhavebeenmadewithadierenttransformationthanthenewanatomicaldataset onwhichtheywillbeoverlaid.

Theonlytimethisdestructionisinappropriateiswhenthefunctionaldatasetsinthe transformedviewarenotinfacttransformationsfromoriginaldatasetsinthesamesession. Thiscouldhappenifyoucopiedatlrcdatasetintoasessionfromanotherdirectoryor ifyoucreatedatlrcdatasetusingdmergesayAFNIwillnotdeleteadatasetifthere isnoparentdatasetfromwhichitwaswarped.

AFNIwillnotletyoumarkandtransformmorethanoneanatomicaldatasetpersession. Onceyouhavetransformedonedatasetinasessiontheotherswillbeolimitstodirect markingandtransformationTheirtransformationswillbederivedfromthemasterdataset thatyoumarkrst.

DefineFunctionandDefineDatamodecontrolpanels

DefineFunction

Thebuttonsandotherwidgetsonthiscontrolpanelareusedtomanipulatehowfunctional datasetsaredisplayedintheviewerwindows.

ThresholdSlider

Ifthecurrentfunctionaldatasethasathresholddatasubbrickieisnotofthefimtype, thentherstitemintheFunctioncontrolpanelisasliderthatletsyouselectthethresholdto applyOnlyvoxelswhoseassociatedvalueisequaltoorabovethisthresholdwillbeoverlaid incolorIfthefunctionaldatasettypeisficofittorfiftthenAFNIknowshowto interpretthethresholdlevelintermsofthestandardnormalmodelsforthesestatistics, andwillshowthecorrespondingpvaluepervoxeljustbelowthesliderThedataset thresholdtypeisshownatthetopoftheslider.

IfthefunctionaldatasetisofthefimtypethenthissliderwillnotbevisibleInthis casetheleftmostitemintheFunctionpanelwillbe:

ColorPbar

Themulticoloredverticalbarwithnumericallabelstotherightandanumberselector labeledbelowiscalledthepbarafteritsnameintheCcodeThisdevicecontrols thecolorsforthefunctionaloverlay.

Thenumberselectorbeneaththepbarcontrolhowmanycolorpanesarepresentfrom toareavailablethedefaultinAFNIissettopanesJustbelowthatisatoggle switchPosThisallowsyoutospecifythatonlypositivevalueswilltheshowninthecolor pbarorthatbothpositiveandnegativevalueswillbeshownSomefunctionaldatasetsare naturallynonnegativefortheseallocatingcolorstothenegativerangeispointless)

ThecolorinanypanemaybealteredbyclickinginsidethepaneitselfAchooserwill thenpopuptoletyouselectfromtheavailablepalettewhichishardcodedintoAFNIand canonlybechangedviatheXdefaultsleOnecolorchoiceisnonewhichmeansthat nocolorwilldisplayforthatrangeoffunctionalintensitieseveniftheyappearinvoxels thatareovertheselectedthreshold.

EachcolorpaneappliestotheindicatedrangeoffunctionalintensitiesTheseintensities arerelativetotheRangecontrolsettingstothelowerrightTheRangesettingisismapped toonthepbarandallotherpbarsettingscorrespondtothesimilarlyscaledvalues inthefunctionaldatasetsubbrickbeingviewedYoumayclickanddragonthesashes' betweenthecolorpanestochangetheintensitythresholds.

Options

TheoptionscolumnisagrabbagoffunctionaldatasetstuTherstboxedsetofbuttons Anatunderlayetcletsyouchoosewhethertheanatomicaldatasetorthefunctional datasetappearsasthebackgroundgrayscaleimagesintheviewingwindowsThesecond boxedsetFuncIntensityetcletsyouchoosebetweendisplayingtheintensityorthe thresholdasthecolordeterminingfunction.

ThethirdboxedsetcomprisedtherangecontrolsforthefunctionalcoloringAtthetop aretheminimumandmaximumvaluesfoundinthecurrentdatasetscfauxiliaryprogram xxxx

dinfoThenextcontrolisatogglelabeledautoRangeThevaluerepresented byxxxxistheautomaticallyassignedrangeforthefunctionalrangewhichcorrespondsto onthepbarThisautoRangeischosenbyAFNIasthelargestabsolutevalueinthe datasetsubbrickIfthetoggleisothenthecontrolbelowisactivatedandallowsyou tospecifythefunctionalvaluethatmapstoonthepbarControllingthisrangemay bedesirablewhencomparingseveraldatasets.

ThelowestsofarcontrolinthiscolumnprovidesanotherFIMmenubuttonseethe GraphsectionThelabeltotherightofthisbuttonshowsthedatasetthatwillbeprocessed oncetheComputeFIMbuttonispressed.


This							control																							column																				determines																																	how											datasets																									are											manipulatedby																																			AFNI																		It				also									contains
some									miscellaneous																																						controls																								that															didnt																		t										in											elsewhere.
																Resampling
	!	Thetopb																						oxedsetofcontrolsletsyouchoosehowtheanatomicaldatathatisactuallydis
Warpondemand		playedwillbegenerated																																																							YoucanviewthedatadirectlyfromtheBRIKleifitisavailable.
subvoxel		Inthiscaseyouarelimitedtoseeingthedatasetatthevoxelresolutionatwhichthedata
markers		wasgenerated																																		Alternatively																																						y		oucanchoose																																								Warp																Anat												on								Demand																	viewingwhichmeans
		that			the																	data											willb													e						interpolated																																					from													its										source																	to							whatever																					resolution																					you										order												using
		thecontrolsjustbelow																																																						Inthiswayitispossibletoplacemarkersatsubvoxellocations.
		AtpresentAFNI																																															cannotdisplaygraphsfromawarpondemanddataset																																																												Ifyoutake																			a					n
		action													that													causes																a					Dtimedataset																																															to										b			e						switched																								to						warpondemand																																					mode												then											any
		open						graph																				windows																							willb												e					destroyed																																This																	willhappen																															for								example																				if			you											switch												from
		orig											totlrc																									view															andhave																											notyet																				writtentheDtimedatasettodisk.
	!	Theinterpolationmodesarenearestneighb																																																														or												NNlinearLicubicCuandblocky'
Resampling modes		BkthislatterisintendedmainlyforfunctionaldatasetsandisintermediatebetweenNN
		andLi																		itsmathematicaldenitionisattheendofthismanual																																																													NNLi																andBkarefairly
		rapidonadecentworkstationbutCucanb																																																														e					noticeablyslow																																							Sinceitusesneighboring
		grid		p						oin											ts						to							interpolate																												vs																			for											Li						and															Bk											and									it							uses									more													complex																		formulas																				this									is
		understandable																																					FormostpurposesLiinterpolationforanatomicalimagesandBkinterpo
		lation										for													functional																							images																					will															b			e			the											best																	NB																	threshold																							data										in							functional																						datasets
		is	always																					resampled																								using																the														NN										mode																			This																is			because																					it							is					somewhat																						unreasonable																										to
		interpolateanonlinearstatisticsuchascorrelationcoecientbetweenvoxelsandthento
		interpret																					thisstatisticusingprobabilisticmodelsthatassumeindependence.
		The															smallest																						resolution																											allowed																									by						the														Resam																	mm															selector																		is														mm												This												is					very
		tiny				and																		imageswilldisplayvery																																																													slowly																				Youcan																								do							itifyou																			wish												however																				donttry																			to
		write								out														a				whole														human																		head																			dataset																				to									disk													at						this														resolution																							The										disk												space										required
		would												b					e					rather																large.
		Controls																										for									determining																																	whether																							the												functional																													dataset																			BRIK														if						available																						or						warp
		ondemand																										will										b		e					used													for														computing																															the											functional																												slices													are								the							next														set							down												The
		functionalBRIK																																						canb														e	used																				onlyifitactuallyexists																																																								inthe															current																	viewiecoordinate
		systemandifitisatthesamespatialresolutionastheanatomicaldatasetbeingviewed.
																Dataset																									Output																								and																	Input
		TheWritebuttonswillcomputeandwritetheBRIKlestodiskfortheindicateddatasets.
		Thecurrentresamplingmodeandresamplingdimensionwillbeusedforthispurpose																																																														The
		Anat									button																					will											output																		the																current																			anatomical																																			dataset																			the										Func												button																	outputs																	the
		current																functional																									dataset																								The																		Many											button																								allows																		you								to								select												more											than															one						dataset
		fromallsessionsandwritethemallout																																																														Thisnewcontrolisprovidedsincetheresampling
		process																can											b		e				relatively																								slow																											now									you															can												select															many														datasets																				start														their								output															in
		TalairachcoordinatesandthengogetsomethinggoodtoeatwhileAFNI																																																														churnsaway.
		MCWAFNI																								2.00																																															{																																																								Dec6

! AFNIwillnotwriteoveradatasetBRIKwhichcannotberecreatedbywarpingfroma

parentThisprecautiondoesnotextendtopluginswhichcanbewrittensoastodestroy

unrecoverableBRIKsItispossibletouseAFNItoresampleadatasetintheorigview,

butonlyifthedatasetiswarpondemandfromanotherdatasetasparentThiscanbe

arrangedusingtheddupauxiliaryprogram.

TheRescanbuttonsaredesignedtorereaddatafromdiskTherstoneThiswill rereadthecurrentsessionThisisusefulifyouuseanauxiliaryprogramsuchasdANOVA tocreateanewdatasetoutsideofAFNIandthenwishtoviewitInearlierversionsit wasnecessarytoexitAFNIandrestartittogetnewdatasetsintotheprogramTheAll buttonwillrereadallthesessionsthatwereinitiallyloadedthereisnofacilitytoreadin anentirenewsessionatthistimeFinallytheDbuttonwillrereadthetimeseries directoriesandloadanynewtimeserieslesthatarefound.

ControllerLock

WiththeNewbuttonlowerleftofAFNIcontrollerwindowitispossibletoviewseveral datasetsatonceinseveralsetsofviewingandgraphingwindowsNormallytheviewpointsoftheseparatecontrollersareindependentthatisclickinginthesagittalwindowof controllerAwillchangetheviewpointofAscoronalandaxialwindowsbutwillhave noeectonBsimageandgraphwindows.

Undersomecircumstancesyoumaywishtolocksomecontrollerstogethersothattheir viewerwindowsmoveinunisonThiscanbedonewiththeLockmenuThereisonlyone lockinAFNIThismenudetermineswhichcontrollerwindowsparticipateinthelockIf thespatialviewpointischangedinanywindowthatisaectedbythelockthenAFNIwill attempttojumpallotherlockedwindowstothecorrespondingviewpoint.

InadditiontheLockmenuhasaClearbuttontodetachallcontrollersfromthelock, andanEnforcebuttonwhichcanbeusedtomakeallviewerwindowsaectedjump tothelockedpositionEnforceisonlyneededjustafterchoosingwhichcontrollersto belockedtogether)

Acoupleofapplicationsforthelock:

ScrollingthroughseveralanatomiesinTalairachcoordinatessimultaneouslyviewing

Trythis

thesimilaritiesanddierences.

ViewingadatasetinOriginalandTalairachcoordinatessimultaneously.

Comparingseveraldierentfunctionaldatasetsoverlaidonthesameanatomy.

AFNIcanhavetroublewhenthelockisusedbetweencontrollersindierentcoordinatesystemsThelocksubroutinewillworkproperlyifthedatasetbeingviewedinonecontrolleris justtherealizationoftheothercontrollersdatasetinadierentcoordinatesystemitwill carryouttheTalairachtransformationoritsinverseasneededtokeepthelockanatomically reasonableItwillfailifthetwocontrollershavedierentcoordinatesystemsanddierent datasetsforexampleitdoesntknowhowtotransformfromTalairachcoordinatesinone datasettoOriginalcoordinatesinanotherdataset.

Plugins

ThelastitemintheDatamodecontrolpanelisthePluginsmenubuttonThiswillonly bepresentifAFNIiscompiledwithpluginsupportandiftheprogramndsatleast onepluginwhenitstartsup.

PluginsareexternalCfunctionswritteninconformancewiththepluginsmanualthat provideextrafunctionalitytoAFNITheyarecompiledintosharedobjectsorshared librarieswiththelenamesuxsoorslonHPUXAFNIsearchesforthemina setofdirectoriesspeciedintheshellenvironmentvariableAFNIPLUGINPATHIfthisisnot denedthenPATHisusedthatwaystoringthecompiledpluginsinthesameplaceasthe MCWAFNIexecutableswillwork.

EachpluginwillcreateoneormoreinterfacepanelsWhenyouselectapluginfrom thePluginsmenuitsinterfacepanelwillpopupAtthatpointyoullinthedesired parametersandthenexecutetheactualplugincodewithoneoftheRunbuttons.

Clusteringpluginplugclustcinterfacepanel

Commandlineswitc hes

ThegeneralformfortheAFNIcommandlineis

afnioptionssessiondirectory]

wheretheoptionslistedbelowallstartwiththecharacterIfnosessiondirectoriesare enteredthentheprogramactsasiftheuserhadtypedforthesessionwhichmeans thatthecurrentworkingdirectorywillbescannedfordatasets.

WhatIconsidertobethemoreusefuloptionsarelistedbelowAcompletelistcanbe foundbyenteringthecommandafnihelp.

purge

ConservesmemorybypurgingdatasetstodiskwhennotinuseUsethisifyourunout ofmemorywhenrunningAFNIThiswillslowthecodedownsouseonlyifneeded.

AnotherapplicationforthepurgeswitchariseswhenusingUnixsymboliclinksto makeadatasetappearasifitisinmorethanonesessiondirectoryatoncewithout copyingthebrickleForexamplesupposeonecreatesusingdmergeanaveraged

anatomicaldatasetGRPtlrcHEADandGRPtlrcBRIKfromsessionsfredethel, andlucyThiscouldbedonefromthedirectoryabovethesessionsbythecommands

dmergeprefixGRPgmeananattlrcHEAD

lnsGRPtlrcHEADfredGRPtlrcHEAD

lnsGRPtlrcBRIKfredGRPtlrcBRIK

lnsGRPtlrcHEADethelGRPtlrcHEAD

lnsGRPtlrcBRIKethelGRPtlrcBRIK

lnsGRPtlrcHEADlucyGRPtlrcHEAD

lnsGRPtlrcBRIKlucyGRPtlrcBRIK

ThelnscommandsputlinkstotheGRPanatomydatasetintoeachofthesession directoriesInthiswayiftheuserrunsAFNIwiththecommand

afnifredethellucy

theneachofthesessionswillhaveaccesstotheGRPdatasetbuttherewillonlybeone physicalcopyofitondisk.

AproblemariseswiththisschemebecauseofthemannerinwhichAFNIaccesseslarge bricklesTheprogramwillnotrecognizethatthelinkspointtothesameactualle, anditwillattempttommaptheGRPtlrcBRIKlemorethanonceThiswilllikely failandtheprogramwillcrashwhenthesecondaccessisattemptedwhentheuser switchestothesecondsession.

UsingthepurgeswitchwillavoidthisproblemBeforeanewdatasetisaccessed whenswitchingsessionsanatomiesorfunctionsexistingdatasetbrickswillbebe munmapedThiswillpreventtheattempttommapthesamebrickletwiceatthesame instant.

AnotherwaytoapproachthisproblemwouldbethroughtheuseoftheddupprogramtocreatewarpondemandcopiesoftheGRPtlrcdatasetineachofthesession directories.

R RecursivelysearcheseachsessiondirectoryformoresessionsubdirectoriesThis willdescendtheentirelesystemhierarchyfromeachsessiondirectorygivenonthe commandlineOnalargediskthismaytakealongtimeTolimittherecursionto5 levelsforexampleuseR.

ignoreN TellstheprogramtoignoretherstNpointsintimeseriesforgraphsandFIMcalculations.

unique

TellstheprogramtocreateauniquesetofcolorsforeachAFNIcontrollerwindowThis allowsdierentdatasetstobeviewedwithdierentgrayscalesorcolorscalesunique willonlyworkonbitPseudoColordisplaysforexampleSGIworkstations.

ncolorsnn TellsAFNItousenngraylevelsfortheimagedisplaysdefaultisSinceAFNI alwaysusesthedefaultcolormaponabitgraphicssystemyoumayrunoutofcolors ifyourunseveralgraphicsprogramsatonceWWWbrowsersarenotoriousforcausing thisproblemsincetheyusuallyallocatemanycolormapentriesandholdontothem justlikeAFNIdoes.

T ec hnicalNotes

TheMCWAFNIpackageisdistributedasacompressedUnixtarleafnitgzItis unpackedwiththecommand

gzipdcafnitgztarxf

TheleswillgointoadirectorynamedAFNI. AFNIrequiresanANSICcompilerXRandMotifItalsorequiresthatthe defaultXVisualbeanorbitPseudoColorvisualtheprogramwillnotworkwith anythingelseThisisordinarilynotaproblemexceptonverylowendandveryhighend workstationsandorXterminals. SeveralMakefilesareincludedinthedistributionThemachinestheyareintendedfor areindicatedbytheirlenamesuxIngeneralyouwillhavetomodifyoneofthese totyourneedsYoumayalsoneedtoeditthelemachdephtosetuptheagsfor themmaproutineappropriately. CopytheappropriateletobeMakefileExamineittomakesurethatitmakessense onyoursystemTobuildtheexecutablesusethecommandmakeallIfyousetthe INSTALLDIRmacrocorrectlyintheMakefilethenmakeinstallwillmvtheexecutable imagestotheirnalrestingspotAfterthatamakecleanisappropriate. TomakeandinstallthepluginssuppliedwithAFNIthecommandsmakepluginsand makeinstallpluginswillworkNotallsystemspecicMakefileshavethecommands neededtocompilepluginsThisisbecauseIdonothaveaccesstosuchcomputersystems. ThereareundoubtedlystillbugsinthissoftwareSuggestionsforfurtherimprovements willbegladlyreceivedbutnoactiononsuchsuggestionscanbeguaranteedTheemail addressforAFNIcommentsisrwcoxmcwedu.

mmaping

AFNIusestheUnixfunctionmmaptoaccesstheBRIKlesThisiswhatmakesitpossible toreadinmanylargedatasetsandnotchokethememoryorswapspaceofthecomputer. Dataisonlyreadfromdiskusingmmapallwritesaredoneusingfwrite.

IfyouneedtodisabletheuseofmmapedittheleddatahanddefineMMAPTHRESHOLD tobeThiswillmakeAFNIusemallocandfreadtoaccesstheBRIKdataThiswill alsostronglylimitthenumberofdatasetsthatcanbeused.

IfyoureceiveamessagethatAFNIcannotloadadatasetintomemoryormmapit, thenyoushouldrestarttheprogramwiththepurgeoptionThiswillforcedatasetsnot

inimmediateusetobepurgedfrommemoryandtobemunmapedwhichmightsolveyour problemThiswillalsomaketheprogramrunslowerwhenyouswitchbetweendatasets.

machdeph

ThisCheaderlecontainsmachinespecicsettingsIfyouareportingAFNItoasystem notavailableatMCWyouwillhavetocreateaMakefileappropriateforyourcomputer, andwillhavetoeditmachdephtosetvariousagscorrectlyInparticularagsformmap anddynamicloadingofpluginsmustbesetcorrectlyCommentsinthisledescribethe optionsthatareavailable.

XResourcesforAFNI

IncludedintheMCWAFNIdistributionisalecalledAFNIXdefaultsThiscontains examplesofhowvariousfeaturesofAFNIcanbecontrolledusingXresources.

FormulaforBkResampling

Denethecardinalbasisfunction

8 �

x^⁴jxj^¹

2 1

�

xjxjjxj1

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jxj

ThenblockyinterpolationinDofafunctiondenedonagridwithspacingsxyz) toanarbitrarypointinspaceis

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XXXxixyjyzkz

fxyzfixjykz:

xyz

ijk

Theactualimplementationofinterpolationisdoneinasomewhatdierentfashionforthe sakeofeciencySeethesourcecodeinafnislicec.

Ac kno wledgemen ts

ManythankstoJimHydeformuchsupportandmanydiscussionsonthedirectionof FMRIanalysesThanksalsoareduetoAndrzejJesmanowiczforforgingthewaywith AFNIsgrandfatherFDDougWardhascontributedalotwiththedmanddANOVA programsnewfeaturesindmergeplusthecreationoftheauxiliaryprogramsmanualMike Beauchamphasaidedimmeasurablybytestingearlierversionsofthissoftwareandbycoming upwithmanyusefulideasJayKummercontributedtheinitialideaforpluginsManyother peopleatMCWhavealsohelpedparticularlywithquickquestionsyouknowwhoyou areandtheoccasionalwarmpumpernickelbagelThisworkwaspartlysupportedbythe UnitedStatesNIHthroughgrantsMHandNSforwhichIamalsograteful.

MCWAFNI2.00 { Dec6

References

JeanTalairachandPierreTournouxCoPlanarStereotaxicAtlasoftheHumanBrain, ThiemeMedicalPublishersNewYork.

PeterABandettiniAndrzejJesmanowiczEricCWongandJamesSHydeProcessingstrategiesfortimecoursedatasetsinfunctionalMRIofthehumanbrainMagn. ResonMed.

RobertWCoxAFNISoftwareforanalysisandvisualizationoffunctionalmagnetic resonanceneuroimagesComputersandBiomedicalResearch.

RobertWCoxAndrzejJesmanowiczandJamesSHydeRealtimefunctionalmagneticresonanceimagingMagnResonMed.

Disclaimer:

MCWAFNIitsassociatedprogramsanditsdocumentationareprovidedasisandnowarranty fortheircorrectnessorusefulnessforanypurposeismadeorimpliedbytheMedicalCollegeofWisconsinMCWorbytheauthorofthesoftwareNeitherMCWnortheauthoracceptsanyliability foranydefectsinthissoftwareoritsmanualsorforanydamagescausedbyuseofthissoftware.

OwnershipConditionsofUseandRestrictions:

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PermissionisgrantedtomakeuseofandtomakecopiesoftheMCWAFNIsoftwareand documentationfornoncommercialresearchpurposesonlyOwnershipofMCWAFNIand allcopiesisretainedbytheMedicalCollegeofWisconsin.

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PatientcareapplicationsarenotrecommendedMCWAFNIhasnotbeenevaluatedbyor approvedbytheUnitedStatesFoodandDrugAdministration.

�

Useforanypurposebyforprotorganizationsisprohibitedwithoutpriorarrangementand writtenpermission.

�

RedistributionofMCWAFNIoranyderivedworkoutsidethereceivinginstitutionis prohibitedwithoutpriorpermission.

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Copiesmaybemadewithinthereceivinginstitutionwithoutseparatepermissionfromthe MedicalCollegeofWisconsin.

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TechnicalsupportegthexingofbugsforMCWAFNIisnotguaranteed.

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