arf3DS4: Activated Region Fitting, fMRI data analysis (3D).
Version 2.5-10

Activated Region Fitting (ARF) is an analysis method for fMRI data.

Browse man pages Browse package API and functions Browse package files

AuthorWouter D. Weeda
Date of publication2014-02-21 11:29:26
MaintainerWouter D. Weeda <w.d.weeda@gmail.com>
LicenseGPL-2
Version2.5-10
URL http://arf.r-forge.r-project.org/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("arf3DS4")

Man pages

arf3DS4-package: Activated Region Fitting fMRI data analysis
arfcorrelation-class: Class "arfcorrelation"
arf-example-data: Activated Region Fitting Example Dataset
arfversion: Check the version of ARF objects.
BIC: Bayesian Information Criterion
checkSolution: Check the integrity of an ARF model
clearWarnings: Clear warnings of a model object.
createAllAverages: Create Averages of runs for all conditions.
createAverages: Create averages of runs for a condition.
createRegs: Create registration directories for runs of an ARF condition.
data-class: arf3DS4 "data" class
determineStartRect: Calculate starting values for an ARF model
differenceCor: Calculate if correlations differ.
euclidDist: Calculate Euclidian distances of all regions in a model.
experiment-class: arf3DS4 "experiment" class
extr-repl-fmridata: Extract/replace elements of an fmri.data object
fitConnectivity: Estimate connectivity of an ARF model
fitModel: Fit an ARF model.
fitRange: Fit a range of models.
fmri2array: Convert fMRI data to an array
fmri.data-class: arf3DS4 "fmri.data" class
functional-class: arf3DS4 "functional" class
getAtlasLabels: Find anatomical atlas labels.
getExp: Access experiment variables.
getModelAtlas: Get Atlas Labels for an ARF model.
loadData: Load an arf3DS4 "data" object.
loadExp: Load an arf3DS4 experiment
loadFunc: Load functional data for a single run of a condition.
loadModel: Load an ARF model
loadOptions: Save/load ARF Options
loadRda: Load an .Rda file into a specified object.
loadReg: Load a registration object.
loadStart: Save/load ARF starting values
makeDerivs: Calculate analytical first-order derivatives of parameters in...
makeExpDirs: Make Experiment directories.
makeLowResStruct: Make low resolution structural image from high resolution T1...
makeROImask: Mask an fMRI image
makeSingleTrialEvents: Estimate single-trial fMRI activity.
mcpCorrect: Calculate Multiple Comparison Corrections
minBIC: Calculate BIC values for multiple ARF models.
mnames-class: arf3DS4 "mnames" class
model-class: arf3DS4 "model" class
newModel: Create a new ARF model
nifti.fileinfo-class: arf3DS4 "nifti.fileinfo" class
nifti.header-class: arf3DS4 "nifti.header" class
options-class: arf3DS4 "options" class
processModel: Process an ARF model.
processSeed: Process a model using a seed number of regions
pruneModel: Prune a model based on invalid gradients and bounded...
readData: read in a NIFTI/ANALYZE file.
readDerivs: Read (binary) derivative file
registration-class: arf3DS4 "registration" class
RMSEA: Calculate Root Mean Square Error.
roiConnectivity: calculate Connectivity with spatial averaging
saveFunc: Save functional object.
saveModel: Save a model object
saveModelBin: Save ARF model estimates to a NIFTI file.
saveReg: Save a registration object
sequence-class: arf3DS4 "sequence" class
setFuncTimings: Set the timings of the stimuli and link to raw time-series.
setIsoContour: Create isocontours
setRegFiles: Set registration files.
setRegParams: Set the registration parameters.
settings-class: arf3DS4 "settings" class
showModels: List all models for a subject/condition.
varcov: Calculate (co)variance matrix of an ARF model.
version-class: arf3DS4 "version" class
wald: Calculate Wald statistics for an arf model.
wald-class: arf3DS4 "wald" class
writeData: Write NIFTI/ANALYZE files.

Functions

.arfcorrelation.corr,arfcorrelation-method Man page
.arfcorrelation.corr.pval,arfcorrelation-method Man page
.arfcorrelation.corr.pval<-,arfcorrelation-method Man page
.arfcorrelation.corr<-,arfcorrelation-method Man page
.arfcorrelation.num.corr,arfcorrelation-method Man page
.arfcorrelation.num.corr<-,arfcorrelation-method Man page
.arfcorrelation.pacorr,arfcorrelation-method Man page
.arfcorrelation.pacorr.pval,arfcorrelation-method Man page
.arfcorrelation.pacorr.pval<-,arfcorrelation-method Man page
.arfcorrelation.pacorr<-,arfcorrelation-method Man page
.arfcorrelation.timebyreg,arfcorrelation-method Man page
.arfcorrelation.timebyreg<-,arfcorrelation-method Man page
.data.avgWfile,data-method Man page
.data.avgWfile<-,data-method Man page
.data.avgdatfile,data-method Man page
.data.avgdatfile<-,data-method Man page
.data.avgtstatFile,data-method Man page
.data.avgtstatFile<-,data-method Man page
.data.betafiles,data-method Man page
.data.betafiles<-,data-method Man page
.data.dataHeader,data-method Man page
.data.dataHeader<-,data-method Man page
.data.fullpath,data-method Man page
.data.fullpath<-,data-method Man page
.data.funcDir,data-method Man page
.data.funcDir<-,data-method Man page
.data.funcRda,data-method Man page
.data.funcRda<-,data-method Man page
.data.mask,data-method Man page
.data.mask<-,data-method Man page
.data.n,data-method Man page
.data.n<-,data-method Man page
.data.name,data-method Man page
.data.name<-,data-method Man page
.data.regDir,data-method Man page
.data.regDir<-,data-method Man page
.data.regRda,data-method Man page
.data.regRda<-,data-method Man page
.data.runs,data-method Man page
.data.runs<-,data-method Man page
.data.ss,data-method Man page
.data.ss<-,data-method Man page
.data.version,data-method Man page
.data.version<-,data-method Man page
.data.weightfiles,data-method Man page
.data.weightfiles<-,data-method Man page
.example Man page
.experiment.avgDir,experiment-method Man page
.experiment.avgDir<-,experiment-method Man page
.experiment.avgWFile,experiment-method Man page
.experiment.avgWFile<-,experiment-method Man page
.experiment.avgdatFile,experiment-method Man page
.experiment.avgdatFile<-,experiment-method Man page
.experiment.avgtstatFile,experiment-method Man page
.experiment.avgtstatFile<-,experiment-method Man page
.experiment.betaDir,experiment-method Man page
.experiment.betaDir<-,experiment-method Man page
.experiment.condition.names,experiment-method Man page
.experiment.condition.names<-,experiment-method Man page
.experiment.condition.num,experiment-method Man page
.experiment.condition.num<-,experiment-method Man page
.experiment.conditionDir,experiment-method Man page
.experiment.conditionDir<-,experiment-method Man page
.experiment.conditionPrefix,experiment-method Man page
.experiment.conditionPrefix<-,experiment-method Man page
.experiment.dataDir,experiment-method Man page
.experiment.dataDir<-,experiment-method Man page
.experiment.dataRda,experiment-method Man page
.experiment.dataRda<-,experiment-method Man page
.experiment.derivativeFile,experiment-method Man page
.experiment.derivativeFile<-,experiment-method Man page
.experiment.expRda,experiment-method Man page
.experiment.expRda<-,experiment-method Man page
.experiment.funcDir,experiment-method Man page
.experiment.funcDir<-,experiment-method Man page
.experiment.funcRda,experiment-method Man page
.experiment.funcRda<-,experiment-method Man page
.experiment.logFile,experiment-method Man page
.experiment.logFile<-,experiment-method Man page
.experiment.lowresAvg,experiment-method Man page
.experiment.lowresAvg<-,experiment-method Man page
.experiment.lowresFile,experiment-method Man page
.experiment.lowresFile<-,experiment-method Man page
.experiment.modelDataFile,experiment-method Man page
.experiment.modelDataFile<-,experiment-method Man page
.experiment.modelDir,experiment-method Man page
.experiment.modelDir<-,experiment-method Man page
.experiment.modelPrefix,experiment-method Man page
.experiment.modelPrefix<-,experiment-method Man page
.experiment.modelRda,experiment-method Man page
.experiment.modelRda<-,experiment-method Man page
.experiment.modeldatDir,experiment-method Man page
.experiment.modeldatDir<-,experiment-method Man page
.experiment.modelnamesRda,experiment-method Man page
.experiment.modelnamesRda<-,experiment-method Man page
.experiment.name,experiment-method Man page
.experiment.name<-,experiment-method Man page
.experiment.optionsRda,experiment-method Man page
.experiment.optionsRda<-,experiment-method Man page
.experiment.path,experiment-method Man page
.experiment.path<-,experiment-method Man page
.experiment.regDir,experiment-method Man page
.experiment.regDir<-,experiment-method Man page
.experiment.regRda,experiment-method Man page
.experiment.regRda<-,experiment-method Man page
.experiment.residualFile,experiment-method Man page
.experiment.residualFile<-,experiment-method Man page
.experiment.startRda,experiment-method Man page
.experiment.startRda<-,experiment-method Man page
.experiment.statsDir,experiment-method Man page
.experiment.statsDir<-,experiment-method Man page
.experiment.statsRda,experiment-method Man page
.experiment.statsRda<-,experiment-method Man page
.experiment.subject.names,experiment-method Man page
.experiment.subject.names<-,experiment-method Man page
.experiment.subject.num,experiment-method Man page
.experiment.subject.num<-,experiment-method Man page
.experiment.subjectDir,experiment-method Man page
.experiment.subjectDir<-,experiment-method Man page
.experiment.subjectPrefix,experiment-method Man page
.experiment.subjectPrefix<-,experiment-method Man page
.experiment.version,experiment-method Man page
.experiment.version<-,experiment-method Man page
.experiment.weightFile,experiment-method Man page
.experiment.weightFile<-,experiment-method Man page
.experiment.weightsDir,experiment-method Man page
.experiment.weightsDir<-,experiment-method Man page
.fmri.data.aux_file,fmri.data-method Man page
.fmri.data.aux_file<-,fmri.data-method Man page
.fmri.data.bitpix,fmri.data-method Man page
.fmri.data.bitpix<-,fmri.data-method Man page
.fmri.data.cal_max,fmri.data-method Man page
.fmri.data.cal_max<-,fmri.data-method Man page
.fmri.data.cal_min,fmri.data-method Man page
.fmri.data.cal_min<-,fmri.data-method Man page
.fmri.data.data.signed,fmri.data-method Man page
.fmri.data.data.signed<-,fmri.data-method Man page
.fmri.data.data.type,fmri.data-method Man page
.fmri.data.data.type<-,fmri.data-method Man page
.fmri.data.data_type,fmri.data-method Man page
.fmri.data.data_type<-,fmri.data-method Man page
.fmri.data.datatype,fmri.data-method Man page
.fmri.data.datatype<-,fmri.data-method Man page
.fmri.data.datavec,fmri.data-method Man page
.fmri.data.datavec<-,fmri.data-method Man page
.fmri.data.db_name,fmri.data-method Man page
.fmri.data.db_name<-,fmri.data-method Man page
.fmri.data.descrip,fmri.data-method Man page
.fmri.data.descrip<-,fmri.data-method Man page
.fmri.data.dim_info,fmri.data-method Man page
.fmri.data.dim_info<-,fmri.data-method Man page
.fmri.data.dims,fmri.data-method Man page
.fmri.data.dims<-,fmri.data-method Man page
.fmri.data.endian,fmri.data-method Man page
.fmri.data.endian<-,fmri.data-method Man page
.fmri.data.extension,fmri.data-method Man page
.fmri.data.extension<-,fmri.data-method Man page
.fmri.data.extents,fmri.data-method Man page
.fmri.data.extents<-,fmri.data-method Man page
.fmri.data.filename,fmri.data-method Man page
.fmri.data.filename<-,fmri.data-method Man page
.fmri.data.filetype,fmri.data-method Man page
.fmri.data.filetype<-,fmri.data-method Man page
.fmri.data.fullpath,fmri.data-method Man page
.fmri.data.fullpath<-,fmri.data-method Man page
.fmri.data.glmax,fmri.data-method Man page
.fmri.data.glmax<-,fmri.data-method Man page
.fmri.data.glmin,fmri.data-method Man page
.fmri.data.glmin<-,fmri.data-method Man page
.fmri.data.gzipped,fmri.data-method Man page
.fmri.data.gzipped<-,fmri.data-method Man page
.fmri.data.intent_code,fmri.data-method Man page
.fmri.data.intent_code<-,fmri.data-method Man page
.fmri.data.intent_name,fmri.data-method Man page
.fmri.data.intent_name<-,fmri.data-method Man page
.fmri.data.intent_p1,fmri.data-method Man page
.fmri.data.intent_p1<-,fmri.data-method Man page
.fmri.data.intent_p2,fmri.data-method Man page
.fmri.data.intent_p2<-,fmri.data-method Man page
.fmri.data.intent_p3,fmri.data-method Man page
.fmri.data.intent_p3<-,fmri.data-method Man page
.fmri.data.magic,fmri.data-method Man page
.fmri.data.magic<-,fmri.data-method Man page
.fmri.data.pixdim,fmri.data-method Man page
.fmri.data.pixdim<-,fmri.data-method Man page
.fmri.data.qform_code,fmri.data-method Man page
.fmri.data.qform_code<-,fmri.data-method Man page
.fmri.data.qoffset_x,fmri.data-method Man page
.fmri.data.qoffset_x<-,fmri.data-method Man page
.fmri.data.qoffset_y,fmri.data-method Man page
.fmri.data.qoffset_y<-,fmri.data-method Man page
.fmri.data.qoffset_z,fmri.data-method Man page
.fmri.data.qoffset_z<-,fmri.data-method Man page
.fmri.data.quatern_b,fmri.data-method Man page
.fmri.data.quatern_b<-,fmri.data-method Man page
.fmri.data.quatern_c,fmri.data-method Man page
.fmri.data.quatern_c<-,fmri.data-method Man page
.fmri.data.quatern_d,fmri.data-method Man page
.fmri.data.quatern_d<-,fmri.data-method Man page
.fmri.data.regular,fmri.data-method Man page
.fmri.data.regular<-,fmri.data-method Man page
.fmri.data.scl_inter,fmri.data-method Man page
.fmri.data.scl_inter<-,fmri.data-method Man page
.fmri.data.scl_slope,fmri.data-method Man page
.fmri.data.scl_slope<-,fmri.data-method Man page
.fmri.data.session_error,fmri.data-method Man page
.fmri.data.session_error<-,fmri.data-method Man page
.fmri.data.sform_code,fmri.data-method Man page
.fmri.data.sform_code<-,fmri.data-method Man page
.fmri.data.sizeof_hdr,fmri.data-method Man page
.fmri.data.sizeof_hdr<-,fmri.data-method Man page
.fmri.data.slice_code,fmri.data-method Man page
.fmri.data.slice_code<-,fmri.data-method Man page
.fmri.data.slice_duration,fmri.data-method Man page
.fmri.data.slice_duration<-,fmri.data-method Man page
.fmri.data.slice_end,fmri.data-method Man page
.fmri.data.slice_end<-,fmri.data-method Man page
.fmri.data.slice_start,fmri.data-method Man page
.fmri.data.slice_start<-,fmri.data-method Man page
.fmri.data.srow_x,fmri.data-method Man page
.fmri.data.srow_x<-,fmri.data-method Man page
.fmri.data.srow_y,fmri.data-method Man page
.fmri.data.srow_y<-,fmri.data-method Man page
.fmri.data.srow_z,fmri.data-method Man page
.fmri.data.srow_z<-,fmri.data-method Man page
.fmri.data.toffset,fmri.data-method Man page
.fmri.data.toffset<-,fmri.data-method Man page
.fmri.data.version,fmri.data-method Man page
.fmri.data.version<-,fmri.data-method Man page
.fmri.data.vox_offset,fmri.data-method Man page
.fmri.data.vox_offset<-,fmri.data-method Man page
.fmri.data.xyzt_units,fmri.data-method Man page
.fmri.data.xyzt_units<-,fmri.data-method Man page
.functional.filename,functional-method Man page
.functional.filename<-,functional-method Man page
.functional.fullpath,functional-method Man page
.functional.fullpath<-,functional-method Man page
.functional.functionaldata,functional-method Man page
.functional.functionaldata<-,functional-method Man page
.functional.linkedfile,functional-method Man page
.functional.linkedfile<-,functional-method Man page
.functional.linkedfiles,functional-method Man page
.functional.linkedfiles<-,functional-method Man page
.functional.timings,functional-method Man page
.functional.timings<-,functional-method Man page
.functional.version,functional-method Man page
.functional.version<-,functional-method Man page
.mnames.condition,mnames-method Man page
.mnames.condition<-,mnames-method Man page
.mnames.experiment,mnames-method Man page
.mnames.experiment<-,mnames-method Man page
.mnames.mnames,mnames-method Man page
.mnames.mnames<-,mnames-method Man page
.mnames.subject,mnames-method Man page
.mnames.subject<-,mnames-method Man page
.model.avgWfile,model-method Man page
.model.avgWfile<-,model-method Man page
.model.avgdatfile,model-method Man page
.model.avgdatfile<-,model-method Man page
.model.avgtstatFile,model-method Man page
.model.avgtstatFile<-,model-method Man page
.model.betafiles,model-method Man page
.model.betafiles<-,model-method Man page
.model.convergence,model-method Man page
.model.convergence<-,model-method Man page
.model.dataHeader,model-method Man page
.model.dataHeader<-,model-method Man page
.model.derivativeFile,model-method Man page
.model.derivativeFile<-,model-method Man page
.model.estimates,model-method Man page
.model.estimates<-,model-method Man page
.model.fit,model-method Man page
.model.fit<-,model-method Man page
.model.fullmodelDataFile,model-method Man page
.model.fullmodelDataFile<-,model-method Man page
.model.fullpath,model-method Man page
.model.fullpath<-,model-method Man page
.model.funcDir,model-method Man page
.model.funcDir<-,model-method Man page
.model.funcRda,model-method Man page
.model.funcRda<-,model-method Man page
.model.gradient,model-method Man page
.model.gradient<-,model-method Man page
.model.hessian,model-method Man page
.model.hessian<-,model-method Man page
.model.iterates,model-method Man page
.model.iterates<-,model-method Man page
.model.logFile,model-method Man page
.model.logFile<-,model-method Man page
.model.mask,model-method Man page
.model.mask<-,model-method Man page
.model.minimum,model-method Man page
.model.minimum<-,model-method Man page
.model.modelDataFile,model-method Man page
.model.modelDataFile<-,model-method Man page
.model.modelFile,model-method Man page
.model.modelFile<-,model-method Man page
.model.modeldatapath,model-method Man page
.model.modeldatapath<-,model-method Man page
.model.modelname,model-method Man page
.model.modelname<-,model-method Man page
.model.modelpath,model-method Man page
.model.modelpath<-,model-method Man page
.model.modeltype,model-method Man page
.model.modeltype<-,model-method Man page
.model.n,model-method Man page
.model.n<-,model-method Man page
.model.name,model-method Man page
.model.name<-,model-method Man page
.model.optionsFile,model-method Man page
.model.optionsFile<-,model-method Man page
.model.params,model-method Man page
.model.params<-,model-method Man page
.model.proctime,model-method Man page
.model.proctime<-,model-method Man page
.model.regDir,model-method Man page
.model.regDir<-,model-method Man page
.model.regRda,model-method Man page
.model.regRda<-,model-method Man page
.model.regions,model-method Man page
.model.regions<-,model-method Man page
.model.residualFile,model-method Man page
.model.residualFile<-,model-method Man page
.model.runs,model-method Man page
.model.runs<-,model-method Man page
.model.sandwichmethod,model-method Man page
.model.sandwichmethod<-,model-method Man page
.model.ss,model-method Man page
.model.ss<-,model-method Man page
.model.startFile,model-method Man page
.model.startFile<-,model-method Man page
.model.startval,model-method Man page
.model.startval<-,model-method Man page
.model.valid,model-method Man page
.model.valid<-,model-method Man page
.model.varcov,model-method Man page
.model.varcov<-,model-method Man page
.model.version,model-method Man page
.model.version<-,model-method Man page
.model.wald,model-method Man page
.model.wald<-,model-method Man page
.model.warnings,model-method Man page
.model.warnings<-,model-method Man page
.model.weightFile,model-method Man page
.model.weightFile<-,model-method Man page
.model.weightfiles,model-method Man page
.model.weightfiles<-,model-method Man page
.nifti.fileinfo.endian,nifti.fileinfo-method Man page
.nifti.fileinfo.endian<-,nifti.fileinfo-method Man page
.nifti.fileinfo.extension,nifti.fileinfo-method Man page
.nifti.fileinfo.extension<-,nifti.fileinfo-method Man page
.nifti.fileinfo.filename,nifti.fileinfo-method Man page
.nifti.fileinfo.filename<-,nifti.fileinfo-method Man page
.nifti.fileinfo.filetype,nifti.fileinfo-method Man page
.nifti.fileinfo.filetype<-,nifti.fileinfo-method Man page
.nifti.fileinfo.fullpath,nifti.fileinfo-method Man page
.nifti.fileinfo.fullpath<-,nifti.fileinfo-method Man page
.nifti.fileinfo.gzipped,nifti.fileinfo-method Man page
.nifti.fileinfo.gzipped<-,nifti.fileinfo-method Man page
.nifti.fileinfo.version,nifti.fileinfo-method Man page
.nifti.fileinfo.version<-,nifti.fileinfo-method Man page
.nifti.header.aux_file,nifti.header-method Man page
.nifti.header.aux_file<-,nifti.header-method Man page
.nifti.header.bitpix,nifti.header-method Man page
.nifti.header.bitpix<-,nifti.header-method Man page
.nifti.header.cal_max,nifti.header-method Man page
.nifti.header.cal_max<-,nifti.header-method Man page
.nifti.header.cal_min,nifti.header-method Man page
.nifti.header.cal_min<-,nifti.header-method Man page
.nifti.header.data.signed,nifti.header-method Man page
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.nifti.header.data.type,nifti.header-method Man page
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.nifti.header.data_type,nifti.header-method Man page
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.nifti.header.datatype,nifti.header-method Man page
.nifti.header.datatype<-,nifti.header-method Man page
.nifti.header.db_name,nifti.header-method Man page
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.nifti.header.descrip,nifti.header-method Man page
.nifti.header.descrip<-,nifti.header-method Man page
.nifti.header.dim_info,nifti.header-method Man page
.nifti.header.dim_info<-,nifti.header-method Man page
.nifti.header.dims,nifti.header-method Man page
.nifti.header.dims<-,nifti.header-method Man page
.nifti.header.endian,nifti.header-method Man page
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.nifti.header.extension,nifti.header-method Man page
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.nifti.header.fullpath,nifti.header-method Man page
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.nifti.header.glmax,nifti.header-method Man page
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.nifti.header.glmin,nifti.header-method Man page
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.nifti.header.gzipped,nifti.header-method Man page
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.nifti.header.intent_code,nifti.header-method Man page
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.nifti.header.intent_name,nifti.header-method Man page
.nifti.header.intent_name<-,nifti.header-method Man page
.nifti.header.intent_p1,nifti.header-method Man page
.nifti.header.intent_p1<-,nifti.header-method Man page
.nifti.header.intent_p2,nifti.header-method Man page
.nifti.header.intent_p2<-,nifti.header-method Man page
.nifti.header.intent_p3,nifti.header-method Man page
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.nifti.header.magic,nifti.header-method Man page
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.nifti.header.qoffset_z,nifti.header-method Man page
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.nifti.header.quatern_b<-,nifti.header-method Man page
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.nifti.header.quatern_c<-,nifti.header-method Man page
.nifti.header.quatern_d,nifti.header-method Man page
.nifti.header.quatern_d<-,nifti.header-method Man page
.nifti.header.regular,nifti.header-method Man page
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.nifti.header.scl_inter,nifti.header-method Man page
.nifti.header.scl_inter<-,nifti.header-method Man page
.nifti.header.scl_slope,nifti.header-method Man page
.nifti.header.scl_slope<-,nifti.header-method Man page
.nifti.header.session_error,nifti.header-method Man page
.nifti.header.session_error<-,nifti.header-method Man page
.nifti.header.sform_code,nifti.header-method Man page
.nifti.header.sform_code<-,nifti.header-method Man page
.nifti.header.sizeof_hdr,nifti.header-method Man page
.nifti.header.sizeof_hdr<-,nifti.header-method Man page
.nifti.header.slice_code,nifti.header-method Man page
.nifti.header.slice_code<-,nifti.header-method Man page
.nifti.header.slice_duration,nifti.header-method Man page
.nifti.header.slice_duration<-,nifti.header-method Man page
.nifti.header.slice_end,nifti.header-method Man page
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.nifti.header.slice_start,nifti.header-method Man page
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.nifti.header.srow_x,nifti.header-method Man page
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.nifti.header.srow_y,nifti.header-method Man page
.nifti.header.srow_y<-,nifti.header-method Man page
.nifti.header.srow_z,nifti.header-method Man page
.nifti.header.srow_z<-,nifti.header-method Man page
.nifti.header.toffset,nifti.header-method Man page
.nifti.header.toffset<-,nifti.header-method Man page
.nifti.header.version,nifti.header-method Man page
.nifti.header.version<-,nifti.header-method Man page
.nifti.header.vox_offset,nifti.header-method Man page
.nifti.header.vox_offset<-,nifti.header-method Man page
.nifti.header.xyzt_units,nifti.header-method Man page
.nifti.header.xyzt_units<-,nifti.header-method Man page
.options.adjust.n,options-method Man page
.options.adjust.n<-,options-method Man page
.options.chk.method,options-method Man page
.options.chk.method<-,options-method Man page
.options.chk.range,options-method Man page
.options.chk.range<-,options-method Man page
.options.min.analyticalgrad,options-method Man page
.options.min.analyticalgrad<-,options-method Man page
.options.min.boundlim,options-method Man page
.options.min.boundlim<-,options-method Man page
.options.min.iterlim,options-method Man page
.options.min.iterlim<-,options-method Man page
.options.min.routine,options-method Man page
.options.min.routine<-,options-method Man page
.options.nlm.gradtol,options-method Man page
.options.nlm.gradtol<-,options-method Man page
.options.nlm.steptol,options-method Man page
.options.nlm.steptol<-,options-method Man page
.options.opt.lower,options-method Man page
.options.opt.lower<-,options-method Man page
.options.opt.method,options-method Man page
.options.opt.method<-,options-method Man page
.options.opt.upper,options-method Man page
.options.opt.upper<-,options-method Man page
.options.output.mode,options-method Man page
.options.output.mode<-,options-method Man page
.options.start.maxfac,options-method Man page
.options.start.maxfac<-,options-method Man page
.options.start.method,options-method Man page
.options.start.method<-,options-method Man page
.options.start.vector,options-method Man page
.options.start.vector<-,options-method Man page
.options.sw.type,options-method Man page
.options.sw.type<-,options-method Man page
.options.version,options-method Man page
.options.version<-,options-method Man page
.registration.Aex2hi,registration-method Man page
.registration.Aex2hi<-,registration-method Man page
.registration.Ahi2st,registration-method Man page
.registration.Ahi2st<-,registration-method Man page
.registration.Dex,registration-method Man page
.registration.Dex<-,registration-method Man page
.registration.Dhi,registration-method Man page
.registration.Dhi<-,registration-method Man page
.registration.Dst,registration-method Man page
.registration.Dst<-,registration-method Man page
.registration.OXst,registration-method Man page
.registration.OXst<-,registration-method Man page
.registration.SXhi,registration-method Man page
.registration.SXhi<-,registration-method Man page
.registration.examp2high,registration-method Man page
.registration.examp2high<-,registration-method Man page
.registration.examp2stand,registration-method Man page
.registration.examp2stand<-,registration-method Man page
.registration.example,registration-method Man page
.registration.example<-,registration-method Man page
.registration.filename,registration-method Man page
.registration.filename<-,registration-method Man page
.registration.fullpath,registration-method Man page
.registration.fullpath<-,registration-method Man page
.registration.high2stand,registration-method Man page
.registration.high2stand<-,registration-method Man page
.registration.highres,registration-method Man page
.registration.highres<-,registration-method Man page
.registration.linkedfile,registration-method Man page
.registration.linkedfile<-,registration-method Man page
.registration.standard,registration-method Man page
.registration.standard<-,registration-method Man page
.registration.version,registration-method Man page
.registration.version<-,registration-method Man page
.sequence.best,sequence-method Man page
.sequence.best<-,sequence-method Man page
.sequence.current,sequence-method Man page
.sequence.current<-,sequence-method Man page
.sequence.fit,sequence-method Man page
.sequence.fit<-,sequence-method Man page
.sequence.minimum,sequence-method Man page
.sequence.minimum<-,sequence-method Man page
.sequence.mnames,sequence-method Man page
.sequence.mnames<-,sequence-method Man page
.sequence.regions,sequence-method Man page
.sequence.regions<-,sequence-method Man page
.sequence.valid,sequence-method Man page
.sequence.valid<-,sequence-method Man page
.settings.avgDir,settings-method Man page
.settings.avgDir<-,settings-method Man page
.settings.avgWFile,settings-method Man page
.settings.avgWFile<-,settings-method Man page
.settings.avgdatFile,settings-method Man page
.settings.avgdatFile<-,settings-method Man page
.settings.avgtstatFile,settings-method Man page
.settings.avgtstatFile<-,settings-method Man page
.settings.betaDir,settings-method Man page
.settings.betaDir<-,settings-method Man page
.settings.conditionDir,settings-method Man page
.settings.conditionDir<-,settings-method Man page
.settings.conditionPrefix,settings-method Man page
.settings.conditionPrefix<-,settings-method Man page
.settings.dataDir,settings-method Man page
.settings.dataDir<-,settings-method Man page
.settings.dataRda,settings-method Man page
.settings.dataRda<-,settings-method Man page
.settings.derivativeFile,settings-method Man page
.settings.derivativeFile<-,settings-method Man page
.settings.expRda,settings-method Man page
.settings.expRda<-,settings-method Man page
.settings.funcDir,settings-method Man page
.settings.funcDir<-,settings-method Man page
.settings.funcRda,settings-method Man page
.settings.funcRda<-,settings-method Man page
.settings.logFile,settings-method Man page
.settings.logFile<-,settings-method Man page
.settings.lowresAvg,settings-method Man page
.settings.lowresAvg<-,settings-method Man page
.settings.lowresFile,settings-method Man page
.settings.lowresFile<-,settings-method Man page
.settings.modelDataFile,settings-method Man page
.settings.modelDataFile<-,settings-method Man page
.settings.modelDir,settings-method Man page
.settings.modelDir<-,settings-method Man page
.settings.modelPrefix,settings-method Man page
.settings.modelPrefix<-,settings-method Man page
.settings.modelRda,settings-method Man page
.settings.modelRda<-,settings-method Man page
.settings.modeldatDir,settings-method Man page
.settings.modeldatDir<-,settings-method Man page
.settings.modelnamesRda,settings-method Man page
.settings.modelnamesRda<-,settings-method Man page
.settings.optionsRda,settings-method Man page
.settings.optionsRda<-,settings-method Man page
.settings.regDir,settings-method Man page
.settings.regDir<-,settings-method Man page
.settings.regRda,settings-method Man page
.settings.regRda<-,settings-method Man page
.settings.residualFile,settings-method Man page
.settings.residualFile<-,settings-method Man page
.settings.startRda,settings-method Man page
.settings.startRda<-,settings-method Man page
.settings.statsDir,settings-method Man page
.settings.statsDir<-,settings-method Man page
.settings.statsRda,settings-method Man page
.settings.statsRda<-,settings-method Man page
.settings.subjectDir,settings-method Man page
.settings.subjectDir<-,settings-method Man page
.settings.subjectPrefix,settings-method Man page
.settings.subjectPrefix<-,settings-method Man page
.settings.version,settings-method Man page
.settings.version<-,settings-method Man page
.settings.weightFile,settings-method Man page
.settings.weightFile<-,settings-method Man page
.settings.weightsDir,settings-method Man page
.settings.weightsDir<-,settings-method Man page
.version.build,version-method Man page
.version.build<-,version-method Man page
.version.svnrev,version-method Man page
.version.svnrev<-,version-method Man page
.version.update,version-method Man page
.version.update<-,version-method Man page
.version.version,version-method Man page
.version.version<-,version-method Man page
.wald.consts,wald-method Man page
.wald.consts<-,wald-method Man page
.wald.df1,wald-method Man page
.wald.df1<-,wald-method Man page
.wald.df2,wald-method Man page
.wald.df2<-,wald-method Man page
.wald.pvalues,wald-method Man page
.wald.pvalues<-,wald-method Man page
.wald.stats,wald-method Man page
.wald.stats<-,wald-method Man page
BIC Man page Source code
RMSEA Man page Source code
[,fmri.data-method Man page
[<-,fmri.data-method Man page
approxHessianR Source code
arf2Excel Source code
arf3DS4 Man page
arf3DS4-package Man page
arfcorrelation-class Man page
arfversion Man page Source code
bin2dec Source code
calcHarvardOxfordProbs Source code
calcTalairach Source code
checkBound Source code
checkExp Source code
checkFiles Source code
checkGradientReturn Source code
checkNonSigReturn Source code
checkSolution Man page Source code
checkSolutionReturn Source code
checkVersion Source code
chngRootExp Source code
clearWarnings Man page Source code
correlationTest Source code
createAllAverages Man page Source code
createAverages Man page Source code
createFuncs Source code
createRegs Man page Source code
cropVolume Source code
cropVolumeAuto Source code
data-class Man page
detSigmaDeriv Source code
determineStartRect Man page Source code
determineStartRectSimple Man page Source code
differenceCor Man page Source code
euclidDist Man page Source code
experiment-class Man page
fallOff Source code
fitConnectivity Man page Source code
fitConnectivityFromFiles Source code
fitModel Man page Source code
fitModelOptim Man page Source code
fitRange Man page Source code
fitSimpleModelOptim Man page Source code
flipAxis Source code
fmri.data-class Man page
fmri2array Man page Source code
functional-class Man page
fwhm.filter Source code
getAtlasLabels Man page Source code
getExp Man page Source code
getFSLdata Source code
getFileInfo Source code
getHarvardOxford Source code
getIntent Source code
getModelAtlas Man page Source code
getTalairach Source code
getlocsquare Source code
gradient.gauss Source code
gradient.simple Source code
headToName Source code
highresBlobs Source code
isEdge Source code
listNoHdr Source code
loadData Man page Source code
loadExp Man page Source code
loadFunc Man page Source code
loadModel Man page Source code
loadOptions Man page Source code
loadRda Man page Source code
loadReg Man page Source code
loadStart Man page Source code
makeBWLocations Source code
makeColors Source code
makeDerivs Man page Source code
makeDiscreteImage Source code
makeExample Man page Source code
makeExpDirs Man page Source code
makeLowResStruct Man page Source code
makeLowResStructAvg Man page Source code
makeROImask Man page Source code
makeResiduals Source code
makeSingleTrialEvents Man page Source code
makeWeights Source code
makeWeightsBin Source code
mcpCorrect Man page Source code
minBIC Man page Source code
mnames-class Man page
model-class Man page
model.gauss Source code
model.simple Source code
newFile Source code
newModel Man page Source code
newProgressElement Source code
nifti.fileinfo-class Man page
nifti.header-class Man page
onLoad Source code
options-class Man page
partialCor Source code
persistentBound Source code
plot,fmri.data,missing-method Man page
plot,model,missing-method Man page
processModel Man page Source code
processSeed Man page Source code
pruneModel Man page
readData Man page Source code
readDerivs Man page Source code
readFSLmat Source code
readHeader Source code
readTimings Source code
registration-class Man page
regressAmplitudes Source code
removeNullString Source code
reqFlip Source code
roiConnectivity Man page Source code
saveFunc Man page Source code
saveModel Man page Source code
saveModelBin Man page Source code
saveModelBinSimple Man page Source code
saveOptions Man page Source code
saveReg Man page Source code
saveStart Man page Source code
sequence-class Man page
setAllObjects Source code
setExp Source code
setFuncFiles Source code
setFuncTimings Man page Source code
setIsoContour Man page Source code
setMask Source code
setRegFiles Man page Source code
setRegParams Man page Source code
settings-class Man page
show,data-method Man page
show,experiment-method Man page
show,fmri.data-method Man page
show,mnames-method Man page
show,model-method Man page
show,options-method Man page
show,sequence-method Man page
show,version-method Man page
showModels Man page Source code
sliceColor Source code
ssq.gauss Source code
ssq.simple Source code
standGen Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
standMethod Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
summary,fmri.data-method Man page
truncDouble Source code
tsCor Source code
updateClass Source code
updateModelNames Source code
validStart Source code
varcov Man page Source code
version-class Man page
wald Man page Source code
wald-class Man page
writeData Man page Source code
writeDataPart Source code
writeHeader Source code
writeHeaderPart Source code
writeProgress Source code
xyzt2char Source code

Files

inst
inst/CITATION
src
src/arffunctionlibrary.c
NAMESPACE
data
data/arf-example-data.RData
data/datalist
R
R/displayFunctions.R
R/coordinateFunctions.R
R/onLoad.R
R/experimentFunctions.R
R/covarianceFunctions.R
R/connectivityFunctions.R
R/arfdataFunctions.R
R/fitModelFunctions.R
R/fitModel.R
R/modelFunctions.R
R/mainFunctions.R
R/niftiFunctions.R
R/exportFunctions.R
R/examples.R
R/Methods.R
R/Generics.R
R/ClassDef.R
MD5
DESCRIPTION
man
man/arfcorrelation-class.Rd
man/setFuncTimings.Rd
man/loadRda.Rd
man/arf-example-data.Rd
man/arf3DS4-package.Rd
man/setRegParams.Rd
man/makeSingleTrialEvents.Rd
man/loadExp.Rd
man/processModel.Rd
man/showModels.Rd
man/settings-class.Rd
man/nifti.header-class.Rd
man/varcov.Rd
man/functional-class.Rd
man/fitConnectivity.Rd
man/fitModel.Rd
man/loadModel.Rd
man/determineStartRect.Rd
man/loadData.Rd
man/checkSolution.Rd
man/loadReg.Rd
man/RMSEA.Rd
man/saveModel.Rd
man/model-class.Rd
man/sequence-class.Rd
man/saveModelBin.Rd
man/differenceCor.Rd
man/clearWarnings.Rd
man/mnames-class.Rd
man/readData.Rd
man/fmri.data-class.Rd
man/newModel.Rd
man/experiment-class.Rd
man/makeROImask.Rd
man/minBIC.Rd
man/writeData.Rd
man/fitRange.Rd
man/createAverages.Rd
man/createRegs.Rd
man/mcpCorrect.Rd
man/registration-class.Rd
man/wald-class.Rd
man/saveReg.Rd
man/nifti.fileinfo-class.Rd
man/wald.Rd
man/getModelAtlas.Rd
man/loadStart.Rd
man/options-class.Rd
man/makeDerivs.Rd
man/setRegFiles.Rd
man/extr-repl-fmridata.Rd
man/arfversion.Rd
man/data-class.Rd
man/BIC.Rd
man/fmri2array.Rd
man/setIsoContour.Rd
man/readDerivs.Rd
man/getAtlasLabels.Rd
man/roiConnectivity.Rd
man/version-class.Rd
man/pruneModel.Rd
man/makeExpDirs.Rd
man/euclidDist.Rd
man/saveFunc.Rd
man/loadOptions.Rd
man/processSeed.Rd
man/loadFunc.Rd
man/makeLowResStruct.Rd
man/getExp.Rd
man/createAllAverages.Rd
arf3DS4 documentation built on May 19, 2017, 8:39 p.m.