buildzstat.volume: Build a Posterior Probability Map (PPM) NIFTI volume

In cudaBayesreg: CUDA Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis

Description

buildzstat.volume builds a PPM statistical volume from slices processed by cudaMultireg.volume.

Usage

buildzstat.volume(fbase=NULL, vreg=2, nu.e=3,
  rg=c(NULL,NULL), swap=FALSE, blobsize=3, savedir=tempdir())

Arguments

fbase	If fbase is left unspecified (default NULL), then user datasets need to be provided as input. Otherwise, fbase indicates the dataset prefix of one of the two demo fMRI datasets to use. see read.fmrislice for a detailed description.
vreg	regression variable to represent in PPM; default(vreg=2)
nu.e	d.f. parameter for regression error variance prior (def: 3)
rg	rg=c(first, last): a vector containing the first and last numbers of the sequence of slices to be processed. If rg=c(NULL,NULL) (default), all slices in the volume are processed.
swap	logical variable (default = FALSE) for choosing the right/left data display convention consistent with FSLVIEW
blobsize	numeric value (default=3). Applies spatial contextual information in a 3D immediate neighbourhood for eliminating 3D blobs with less than blobsize active voxels.
savedir	Directory (def: tempdir()) were the MCMC simulations for all slices are saved.

Details

The PPM volume is build by buildzstat.volume after all slices in the desired range rg have been processed by cudaBayesreg.volume. The PPM volume has the dimension of the original volume. However, when a non-null range rg is specified only the slices in the range are statistically processed. The remaining slices are assumed to contain non-activated voxels. To run the examples, the data sets from the R-package cudaBayesregData are required.

Value

nactive

numeric vector containing the number of estimated active voxels for each slice in range rg.

Author(s)

Adelino Ferreira da Silva, Universidade Nova de Lisboa, Faculdade de Ciencias e Tecnologia, Portugal, [e-mail].

References

Adelino R. Ferreira da Silva (2011). “cudaBayesreg: Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis.” Journal of Statistical Software, 44(4), 1–24. URL http://www.jstatsoft.org/v44/i04/.

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.

Adelino Ferreira da Silva (2011). “A Bayesian Multilevel Model for fMRI Data Analysis.”, Computer Methods and Programs in Biomedicine, 102,(3), 238–252.

Adelino Ferreira da Silva (2010). “cudaBayesreg: Bayesian Computation in CUDA.”, The R Journal, 2/2, 48-55. URL http://journal.r-project.org/archive/2010-2/RJournal_2010-2_Ferreira~da~Silva.pdf.

Brandon Whitcher, Volker Schmid and Andrew Thornton (2011). oro.nifti: Rigorous - NIfTI Input / Output, R package version 0.2.5. URL http://CRAN.R-project.org/package=oro.nifti.

See Also

read.fmrislice, buildzstat.volume, cudaMultireg.slice, post.overlay

Examples

## Not run: 
## Simulation using the visual/auditory test dataset "fmri"  
cudaMultireg.volume(fbase="fmri", R=2000, savedir=tempdir())
buildzstat.volume(fbase="fmri", vreg=2)
post.overlay(fbase="fmri", vreg=2, view="axial")
buildzstat.volume(fbase="fmri", vreg=4)
post.overlay(fbase="fmri", vreg=4, view="axial")
##
## simulation using the SPM auditory dataset "swrfM*" 
cudaMultireg.volume(fbase="swrfM", R=2000, rg=c(13,16), savedir=tempdir())
buildzstat.volume(fbase="swrfM", rg=c(13,16))
post.overlay(fbase="swrfM", vreg=2, rg=c(13,16), view="axial")
##

## End(Not run)

cudaBayesreg documentation built on May 29, 2017, 6:19 p.m.