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arf3DS4 (version 2.5-2)

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')

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Version

2.5-2

License

GPL-2

Maintainer

Wouter D Weeda

Last Published

June 28th, 2011

Functions in arf3DS4 (2.5-2)

makeROImask

Mask an fMRI image

loadReg

Load a registration object.

createRegs

Create registration directories for runs of an ARF condition.

arf3DS4-package

Activated Region Fitting fMRI data analysis

processSeed

Process a model using a seed number of regions

makeLowResStruct

Make low resolution structural image from high resolution T1 image.

options-class

arf3DS4 "options" class

BIC

Bayesian Information Criterion

mcpCorrect

Calculate Multiple Comparison Corrections

fitModel

Fit an ARF model.

RMSEA

Calculate Root Mean Square Error.

functional-class

arf3DS4 "functional" class

readData

read in a NIFTI/ANALYZE file.

registration-class

arf3DS4 "registration" class

makeDerivs

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

setIsoContour

Create isocontours

nifti.header-class

arf3DS4 "nifti.header" class

euclidDist

Calculate Euclidian distances of all regions in a model.

createAllAverages

Create Averages of runs for all conditions.

checkSolution

Check the integrity of an ARF model

sequence-class

arf3DS4 "sequence" class

loadRda

Load an .Rda file into a specified object.

loadStart

Save/load ARF starting values

experiment-class

arf3DS4 "experiment" class

loadModel

Load an ARF model

arfcorrelation-class

Class "arfcorrelation"

makeExpDirs

Make Experiment directories.

fitConnectivity

Estimate connectivity of an ARF model

getAtlasLabels

Find anatomical atlas labels.

loadExp

Load an arf3DS4 experiment

saveReg

Save a registration object

setFuncTimings

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

varcov

Calculate (co)variance matrix of an ARF model.

makeSingleTrialEvents

Estimate single-trial fMRI activity.

roiConnectivity

calculate Connectivity with spatial averaging

createAverages

Create averages of runs for a condition.

readDerivs

Read (binary) derivative file

loadOptions

Save/load ARF Options

processModel

Process an ARF model.

mnames-class

arf3DS4 "mnames" class

saveModel

Save a model object

clearWarnings

Clear warnings of a model object.

loadData

Load an arf3DS4 "data" object.

data-class

arf3DS4 "data" class

showModels

List all models for a subject/condition.

arfversion

Check the version of ARF objects.

saveFunc

Save functional object.

version-class

arf3DS4 "version" class

nifti.fileinfo-class

arf3DS4 "nifti.fileinfo" class

fmri.data-class

arf3DS4 "fmri.data" class

getModelAtlas

Get Atlas Labels for an ARF model.

minBIC

Calculate BIC values for multiple ARF models.

getExp

Access experiment variables.

pruneModel

Prune a model based on invalid gradients and bounded parameters.

wald

Calculate Wald statistics for an arf model.

wald-class

arf3DS4 "wald" class

settings-class

arf3DS4 "settings" class

newModel

Create a new ARF model

arf-example-data

Activated Region Fitting Example Dataset

fmri2array

Convert fMRI data to an array

differenceCor

Calculate if correlations differ.

writeData

Write NIFTI/ANALYZE files.

model-class

arf3DS4 "model" class

loadFunc

Load functional data for a single run of a condition.

setRegParams

Set the registration parameters.

saveModelBin

Save ARF model estimates to a NIFTI file.

extr-repl-fmridata

Extract/replace elements of an fmri.data object

determineStartRect

Calculate starting values for an ARF model

fitRange

Fit a range of models.

setRegFiles

Set registration files.