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

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

AuthorWouter D. Weeda
Date of publication2014-02-21 11:29:26
MaintainerWouter D. Weeda <>

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 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 arf3DS4 "" 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.

Files in this package

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

Questions? Problems? Suggestions? or email at

All documentation is copyright its authors; we didn't write any of that.