.example                Activated Region Fitting Example Dataset
BIC                     Bayesian Information Criterion
RMSEA                   Calculate Root Mean Square Error.
[,fmri.data-method      Extract/replace elements of an fmri.data object
arf3DS4-package         Activated Region Fitting fMRI data analysis
arfcorrelation-class    Class "arfcorrelation"
arfversion              Check the version of ARF objects.
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
fitConnectivity         Estimate connectivity of an ARF model
fitModel                Fit an ARF model.
fitRange                Fit a range of models.
fmri.data-class         arf3DS4 "fmri.data" class
fmri2array              Convert fMRI data to an array
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 an ARF model.
makeExpDirs             Make Experiment directories.
makeLowResStruct        Make low resolution structural image from high
                        resolution T1 image.
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 parameters.
readData                read in a NIFTI/ANALYZE file.
readDerivs              Read (binary) derivative file
registration-class      arf3DS4 "registration" class
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.
