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arf3DS4 (version 2.5-4)

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

2.5-4

License

GPL-2

Maintainer

Wouter D Weeda

Last Published

November 2nd, 2011

Functions in arf3DS4 (2.5-4)

euclidDist

Calculate Euclidian distances of all regions in a model.

determineStartRect

Calculate starting values for an ARF model

loadStart

Save/load ARF starting values

RMSEA

Calculate Root Mean Square Error.

loadFunc

Load functional data for a single run of a condition.

makeDerivs

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

setIsoContour

Create isocontours

BIC

Bayesian Information Criterion

getAtlasLabels

Find anatomical atlas labels.

checkSolution

Check the integrity of an ARF model

experiment-class

arf3DS4 "experiment" class

nifti.header-class

arf3DS4 "nifti.header" class

fmri.data-class

arf3DS4 "fmri.data" class

version-class

arf3DS4 "version" class

fitRange

Fit a range of models.

makeLowResStruct

Make low resolution structural image from high resolution T1 image.

readData

read in a NIFTI/ANALYZE file.

createAllAverages

Create Averages of runs for all conditions.

fitConnectivity

Estimate connectivity of an ARF model

saveFunc

Save functional object.

differenceCor

Calculate if correlations differ.

createRegs

Create registration directories for runs of an ARF condition.

clearWarnings

Clear warnings of a model object.

arfcorrelation-class

Class "arfcorrelation"

nifti.fileinfo-class

arf3DS4 "nifti.fileinfo" class

loadRda

Load an .Rda file into a specified object.

setRegParams

Set the registration parameters.

makeExpDirs

Make Experiment directories.

minBIC

Calculate BIC values for multiple ARF models.

loadOptions

Save/load ARF Options

processSeed

Process a model using a seed number of regions

newModel

Create a new ARF model

arf-example-data

Activated Region Fitting Example Dataset

createAverages

Create averages of runs for a condition.

loadExp

Load an arf3DS4 experiment

varcov

Calculate (co)variance matrix of an ARF model.

wald

Calculate Wald statistics for an arf model.

pruneModel

Prune a model based on invalid gradients and bounded parameters.

arf3DS4-package

Activated Region Fitting fMRI data analysis

fmri2array

Convert fMRI data to an array

makeROImask

Mask an fMRI image

setRegFiles

Set registration files.

mcpCorrect

Calculate Multiple Comparison Corrections

saveModelBin

Save ARF model estimates to a NIFTI file.

functional-class

arf3DS4 "functional" class

data-class

arf3DS4 "data" class

setFuncTimings

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

wald-class

arf3DS4 "wald" class

getModelAtlas

Get Atlas Labels for an ARF model.

settings-class

arf3DS4 "settings" class

roiConnectivity

calculate Connectivity with spatial averaging

extr-repl-fmridata

Extract/replace elements of an fmri.data object

options-class

arf3DS4 "options" class

loadData

Load an arf3DS4 "data" object.

mnames-class

arf3DS4 "mnames" class

saveReg

Save a registration object

fitModel

Fit an ARF model.

processModel

Process an ARF model.

registration-class

arf3DS4 "registration" class

getExp

Access experiment variables.

makeSingleTrialEvents

Estimate single-trial fMRI activity.

saveModel

Save a model object

loadReg

Load a registration object.

showModels

List all models for a subject/condition.

sequence-class

arf3DS4 "sequence" class

readDerivs

Read (binary) derivative file

loadModel

Load an ARF model

model-class

arf3DS4 "model" class

writeData

Write NIFTI/ANALYZE files.

arfversion

Check the version of ARF objects.