arf3DS4: Activated Region Fitting, fMRI data analysis (3D).

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

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

View on CRAN

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

arf3DS4 Man page
arf3DS4-package Man page
arfcorrelation-class Man page
.arfcorrelation.corr<-,arfcorrelation-method Man page
.arfcorrelation.corr,arfcorrelation-method Man page
.arfcorrelation.corr.pval<-,arfcorrelation-method Man page
.arfcorrelation.corr.pval,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,arfcorrelation-method Man page
.arfcorrelation.pacorr.pval<-,arfcorrelation-method Man page
.arfcorrelation.pacorr.pval,arfcorrelation-method Man page
.arfcorrelation.timebyreg<-,arfcorrelation-method Man page
.arfcorrelation.timebyreg,arfcorrelation-method Man page
arfversion Man page
BIC Man page
checkSolution Man page
clearWarnings Man page
createAllAverages Man page
createAverages Man page
createRegs 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.avgWfile<-,data-method Man page
.data.avgWfile,data-method Man page
.data.betafiles<-,data-method Man page
.data.betafiles,data-method Man page
data-class 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.name<-,data-method Man page
.data.name,data-method Man page
.data.n<-,data-method Man page
.data.n,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
determineStartRect Man page
determineStartRectSimple Man page
differenceCor Man page
euclidDist Man page
.example Man page
.experiment.avgdatFile<-,experiment-method Man page
.experiment.avgdatFile,experiment-method Man page
.experiment.avgDir<-,experiment-method Man page
.experiment.avgDir,experiment-method Man page
.experiment.avgtstatFile<-,experiment-method Man page
.experiment.avgtstatFile,experiment-method Man page
.experiment.avgWFile<-,experiment-method Man page
.experiment.avgWFile,experiment-method Man page
.experiment.betaDir<-,experiment-method Man page
.experiment.betaDir,experiment-method Man page
experiment-class Man page
.experiment.conditionDir<-,experiment-method Man page
.experiment.conditionDir,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.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.modeldatDir<-,experiment-method Man page
.experiment.modeldatDir,experiment-method Man page
.experiment.modelDir<-,experiment-method Man page
.experiment.modelDir,experiment-method Man page
.experiment.modelnamesRda<-,experiment-method Man page
.experiment.modelnamesRda,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.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.subjectDir<-,experiment-method Man page
.experiment.subjectDir,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.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
fitConnectivity Man page
fitModel Man page
fitModelOptim Man page
fitRange Man page
fitSimpleModelOptim Man page
fmri2array 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-class 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
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.fmri.data.intent_p2<-,fmri.data-method Man page
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.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-method Man page
[,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
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.fmri.data.qoffset_x<-,fmri.data-method Man page
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.fmri.data.qoffset_y<-,fmri.data-method Man page
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.fmri.data.qoffset_z<-,fmri.data-method Man page
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.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-class 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
getAtlasLabels Man page
getExp Man page
getModelAtlas Man page
loadData Man page
loadExp Man page
loadFunc Man page
loadModel Man page
loadOptions Man page
loadRda Man page
loadReg Man page
loadStart Man page
makeDerivs Man page
makeExample Man page
makeExpDirs Man page
makeLowResStruct Man page
makeLowResStructAvg Man page
makeROImask Man page
makeSingleTrialEvents Man page
mcpCorrect Man page
minBIC Man page
mnames-class 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.avgdatfile<-,model-method Man page
.model.avgdatfile,model-method Man page
.model.avgtstatFile<-,model-method Man page
.model.avgtstatFile,model-method Man page
.model.avgWfile<-,model-method Man page
.model.avgWfile,model-method Man page
.model.betafiles<-,model-method Man page
.model.betafiles,model-method Man page
model-class 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.modeldatapath<-,model-method Man page
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.model.modeltype<-,model-method Man page
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.model.name<-,model-method Man page
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.model.n<-,model-method Man page
.model.n,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.regions<-,model-method Man page
.model.regions,model-method Man page
.model.regRda<-,model-method Man page
.model.regRda,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
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.model.startFile<-,model-method Man page
.model.startFile,model-method Man page
.model.startval<-,model-method Man page
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.model.valid<-,model-method Man page
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.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
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.model.warnings<-,model-method Man page
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.model.weightFile<-,model-method Man page
.model.weightFile,model-method Man page
.model.weightfiles<-,model-method Man page
.model.weightfiles,model-method Man page
newModel Man page
nifti.fileinfo-class Man page
.nifti.fileinfo.endian<-,nifti.fileinfo-method Man page
.nifti.fileinfo.endian,nifti.fileinfo-method Man page
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options-class Man page
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plot,fmri.data,missing-method Man page
plot,model,missing-method Man page
processModel Man page
processSeed Man page
pruneModel Man page
readData Man page
readDerivs Man page
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registration-class Man page
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RMSEA Man page
roiConnectivity Man page
saveFunc Man page
saveModel Man page
saveModelBin Man page
saveModelBinSimple Man page
saveOptions Man page
saveReg Man page
saveStart Man page
.sequence.best<-,sequence-method Man page
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sequence-class Man page
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setFuncTimings Man page
setIsoContour Man page
setRegFiles Man page
setRegParams Man page
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settings-class Man page
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.settings.weightsDir<-,settings-method Man page
.settings.weightsDir,settings-method 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
showModels Man page
show,options-method Man page
show,sequence-method Man page
show,version-method Man page
summary,fmri.data-method Man page
varcov Man page
.version.build<-,version-method Man page
.version.build,version-method Man page
version-class Man page
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.version.svnrev,version-method Man page
.version.update<-,version-method Man page
.version.update,version-method Man page
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wald Man page
wald-class Man page
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.wald.pvalues<-,wald-method Man page
.wald.pvalues,wald-method Man page
.wald.stats<-,wald-method Man page
.wald.stats,wald-method Man page
writeData Man page

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

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