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A B C D E F G L M N O P R S V W misc
| arf3DS4-package | Activated Region Fitting fMRI data analysis |
| arf3DS4 | Activated Region Fitting fMRI data analysis |
| arfcorrelation-class | Class "arfcorrelation" |
| 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 |
| determineStartRectSimple | 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. |
| fitModelOptim | Fit an ARF model. |
| fitRange | Fit a range of models. |
| fitSimpleModelOptim | Fit an ARF model. |
| 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. |
| makeExample | Activated Region Fitting Example Dataset |
| makeExpDirs | Make Experiment directories. |
| makeLowResStruct | Make low resolution structural image from high resolution T1 image. |
| makeLowResStructAvg | 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 |
| plot-method | arf3DS4 "fmri.data" class |
| plot-method | arf3DS4 "model" 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 |
| 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. |
| saveModelBinSimple | Save ARF model estimates to a NIFTI file. |
| saveOptions | Save/load ARF Options |
| saveReg | Save a registration object |
| saveStart | Save/load ARF starting values |
| 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 |
| show-method | arf3DS4 "data" class |
| show-method | arf3DS4 "experiment" class |
| show-method | arf3DS4 "fmri.data" class |
| show-method | arf3DS4 "mnames" class |
| show-method | arf3DS4 "model" class |
| show-method | arf3DS4 "options" class |
| show-method | arf3DS4 "sequence" class |
| show-method | arf3DS4 "version" class |
| showModels | List all models for a subject/condition. |
| summary-method | arf3DS4 "fmri.data" class |
| 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. |