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arf3DS4 (version 2.5-10)

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

Description

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

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Version

Install

install.packages('arf3DS4')

Monthly Downloads

18

Version

2.5-10

License

GPL-2

Maintainer

Wouter D Weeda

Last Published

February 21st, 2014

Functions in arf3DS4 (2.5-10)

createRegs

Create registration directories for runs of an ARF condition.
functional-class

arf3DS4 "functional" class
fitModel

Fit an ARF model.
extr-repl-fmridata

Extract/replace elements of an fmri.data object
RMSEA

Calculate Root Mean Square Error.
arfversion

Check the version of ARF objects.
registration-class

arf3DS4 "registration" class
getExp

Access experiment variables.
loadData

Load an arf3DS4 "data" object.
loadStart

Save/load ARF starting values
getModelAtlas

Get Atlas Labels for an ARF model.
saveReg

Save a registration object
minBIC

Calculate BIC values for multiple ARF models.
getAtlasLabels

Find anatomical atlas labels.
euclidDist

Calculate Euclidian distances of all regions in a model.
makeSingleTrialEvents

Estimate single-trial fMRI activity.
readData

read in a NIFTI/ANALYZE file.
loadRda

Load an .Rda file into a specified object.
roiConnectivity

calculate Connectivity with spatial averaging
determineStartRect

Calculate starting values for an ARF model
setFuncTimings

Set the timings of the stimuli and link to raw time-series.
saveModelBin

Save ARF model estimates to a NIFTI file.
pruneModel

Prune a model based on invalid gradients and bounded parameters.
arfcorrelation-class

Class "arfcorrelation"
BIC

Bayesian Information Criterion
makeDerivs

Calculate analytical first-order derivatives of parameters in an ARF model.
makeExpDirs

Make Experiment directories.
loadOptions

Save/load ARF Options
arf-example-data

Activated Region Fitting Example Dataset
newModel

Create a new ARF model
wald

Calculate Wald statistics for an arf model.
data-class

arf3DS4 "data" class
loadReg

Load a registration object.
options-class

arf3DS4 "options" class
createAverages

Create averages of runs for a condition.
nifti.fileinfo-class

arf3DS4 "nifti.fileinfo" class
setRegParams

Set the registration parameters.
nifti.header-class

arf3DS4 "nifti.header" class
readDerivs

Read (binary) derivative file
version-class

arf3DS4 "version" class
setRegFiles

Set registration files.
loadModel

Load an ARF model
wald-class

arf3DS4 "wald" class
clearWarnings

Clear warnings of a model object.
checkSolution

Check the integrity of an ARF model
fitConnectivity

Estimate connectivity of an ARF model
fitRange

Fit a range of models.
saveModel

Save a model object
loadExp

Load an arf3DS4 experiment
sequence-class

arf3DS4 "sequence" class
arf3DS4-package

Activated Region Fitting fMRI data analysis
model-class

arf3DS4 "model" class
processModel

Process an ARF model.
settings-class

arf3DS4 "settings" class
processSeed

Process a model using a seed number of regions
fmri2array

Convert fMRI data to an array
makeROImask

Mask an fMRI image
mcpCorrect

Calculate Multiple Comparison Corrections
mnames-class

arf3DS4 "mnames" class
showModels

List all models for a subject/condition.
setIsoContour

Create isocontours
differenceCor

Calculate if correlations differ.
fmri.data-class

arf3DS4 "fmri.data" class
saveFunc

Save functional object.
makeLowResStruct

Make low resolution structural image from high resolution T1 image.
varcov

Calculate (co)variance matrix of an ARF model.
createAllAverages

Create Averages of runs for all conditions.
experiment-class

arf3DS4 "experiment" class
loadFunc

Load functional data for a single run of a condition.
writeData

Write NIFTI/ANALYZE files.