data-class: arf3DS4 "data" class

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

Description

The "data" class contains all information on the fMRI data of one condition of a subject. Specifically it contains filenames of the datafiles (with full paths) and some basic information of the data, the number of runs, and additional files used by ARF. Each instance of a model class object inherits a "data" object. The "data" class also uses some slots of the experiment class.

Details

The "data" class contains information on the file-locations of the fMRI data. The fMRI data (outcomes of a GLM analysis) must be available in the /beta and /weights directories of each condition for each subject. The data can be in the form of beta-values with associated squared standard errors or t-values with the standard errors set to 1. In the latter case the only files that have to be copied are the t-values to the /beta directory, the weight-files are then created automatically. The average files are created after a call to createAverages.

Objects

Objects can be created by calls of the form new("data", ...).

Slots

name:

Name of the data object, usually 'subjectname - conditionname'.

fullpath:

Full path to the data directory.

betafiles:

Vector of filenames (full paths) of the beta files (containing beta estimates).

weightfiles:

Vector of filenames (full path) of the weight files (containing variances of the beta estimates).

avgdatfile:

Filename of the averaged beta file.

avgWfile:

Filename of the averaged weight file.

avgtstatFile:

Filename of the average t-statistics (=avgbetafile/sqrt(avgweightfile)) file.

n:

Number of 'brain' voxels (excluding voxels not masked).

mask:

Vector containing the mask for the data.

ss:

Sums-of-squares of the data.

regDir:

Full path to the registration directory.

regRda:

Name of the registration.Rda file.

funcDir:

Full path to the functional directory.

funcRda:

Name of the functional.Rda file.

dataHeader:

Nifti header information from the avgdataFile.

runs:

Number of runs (= number of beta files).

version:

Object of class "version" (see version).

Methods

Standard arf3DS4 accessor and replacement functions can be used to access and replace slots.

access

.classname.slotname(object)

replace

.classname.slotname(object)<-

In this case classname is "data" and slotname is for example "avgstatFile". So to access the "avgtstatFile" slot of an r-object "mydata" (of class "data") type .settings.avgtstatFile(mydata).

Author(s)

Wouter D. Weeda - [e-mail]

See Also

model, experiment

Examples

showClass("data")

arf3DS4 documentation built on May 2, 2019, 5:16 p.m.