cudaBayesreg (version 0.3-16)

read.Zsegslice: Read brain segmented data based on structural regions for CSF, gray, and white matter.

Description

read.Zsegslice builds the Z matrix of the statistical model, based on the brain segmented regions CSF/GRY/WHT for a given fMRI dataset.

Usage

read.Zsegslice(slicedata, ymaskdata)

Arguments

slicedata

list of data values returned by the call to read.fmrislice

ymaskdata

list of data values returned by the call to premask

Value

Z

centered matrix specifying the characteristics of cross-sectional units (optional group information)

Details

The FSL tools may be used to obtain the segmented masks for brain parcellation in three main regions according to tissue type (CSF,GRY,WHT). If fbase has been left unspecified in reading slicedata, then three user specified segmented datasets in gzipped NIFTI format must be provided as input, with the names ‘csf.nii.gz’, ‘gry.nii.gz’, and ‘wht.nii.gz’. Otherwise, fbase indicates the dataset prefix of one of the three segmented masks provided as a group effects example for ‘swrfM_filtered_func_data.nii.gz’: ‘swrfM_csf.nii.gz’, ‘swrfM_gry.nii.gz’, and ‘swrfM_wht’. Only swrfM segmented masks are provided in cudaBayesregData. The segmented masks included in the package were obtained by applying FAST to the structural high-resolution image ‘sM00223*’, followed by FLIRT for low-resolution registration to ‘fM00223*’. The ‘sM00223*’ and ‘fM00223*’ datasets are available from the SPM site, and are described in chapter 28 of the SPM8 manual. The fMRI dataset ‘swrfM_filtered_func_data.nii.gz’ is a filtered version of ‘fM00223*’.

References

Adelino Ferreira da Silva (2011). cudaBayesregData: Data sets for the examples used in the package cudaBayesreg, R package version 0.3-10. URL http://CRAN.R-project.org/package=cudaBayesregData.

FSL/FEAT Analysis tool, FMRIB Software Library (FSL). URL www.fmrib.ox.ac.uk/fsl.

John Ashburner et. al.. SPM8 Manual, Functional Imaging Laboratory, Institute of Neurology, UCL, London. URL http://www.fil.ion.ucl.ac.uk/spm/.

See Also

cudaMultireg.slice, post.randeff, premask, post.ppm

Examples

## Not run: 
# fbase <- "swrfM"
# slice <- 21
# slicedata <- read.fmrislice(fbase=fbase, slice=slice, swap=FALSE )
# ymaskdata <- premask(slicedata)
# Z <- read.Zsegslice(slicedata, ymaskdata )
# ## Random effects simulation
# fsave <- paste(tempdir(),"/simultest2",fileext = ".sav", sep="")
# out <- cudaMultireg.slice(slicedata, ymaskdata, R=2000, keep=5, nu.e=3,
#   fsave=fsave, zprior=TRUE)
# post.ppm(out=out, slicedata=slicedata, ymaskdata=ymaskdata, vreg=2)
# 
# ## End(Not run)