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

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

Author
Wouter D. Weeda
Date of publication
2014-02-21 11:29:26
Maintainer
Wouter D. Weeda <w.d.weeda@gmail.com>
License
GPL-2
Version
2.5-10
URLs

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.

Files in this package

arf3DS4
arf3DS4/inst
arf3DS4/inst/CITATION
arf3DS4/src
arf3DS4/src/arffunctionlibrary.c
arf3DS4/NAMESPACE
arf3DS4/data
arf3DS4/data/arf-example-data.RData
arf3DS4/data/datalist
arf3DS4/R
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/MD5
arf3DS4/DESCRIPTION
arf3DS4/man
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/fmri.data-class.Rd
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