R/aaa_data.R

In neuroconductor/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

#' DesikanKillianyTourville
#' 
#' A data frame label numbers and names for the neuroanatomical 
#' DesikanKillianyTourville labels.
#' 
#' @docType data
#' @references  \url{http://www.ncbi.nlm.nih.gov/pubmed/23227001}
#' @format A data frame listing the following variables.
#' \describe{
#'    \item{\code{label_num}}{ Numerical label value. }
#'    \item{\code{label_name}}{ Shorthand anatomical value. }
#'    \item{\code{tissue}}{ Shorthand tissue value. }
#'    \item{\code{contralateral}}{ contralateral anatomical value. }
#'    \item{\code{lobe}}{ which lobe: temporal, parietal, occipital, frontal.}
#'    \item{\code{hemisphere}}{ left or right hemisphere. }
#' }
#' @examples
#' data(DesikanKillianyTourville) 
"DesikanKillianyTourville"

#' BOLD Correlation Matrix
#' 
#' A data frame with an example square BOLD correlation matrix.
#' 
#' @docType data
#' 
#' @format A data frame square correlation matrix listed by AAL 
#' anatomical column names.
#' @references \url{http://en.wikipedia.org/wiki/Automated_Anatomical_Labeling}
#' @examples 
#' data(bold_correlation_matrix)
"bold_correlation_matrix"

#' @title powers_areal_mni_itk
#' @docType data
#' @description A data frame providing coordinates for the nodes 
#' identified by Powers at al. Coordinates have been modified from nifti 
#' space to ITK space
#' @format A data frame listing the following variables.
#' \describe{
#'   \item{\code{x}}{ x coordinate }
#'   \item{\code{y}}{ y coordinate }
#'   \item{\code{z}}{ z coordinate }
#'   \item{\code{ROI}}{ unique integer for each node }
#'   \item{\code{SystemLabel}}{ unique integer for each system }
#'   \item{\code{SystemName}}{ unique name for each system }
#'   \item{\code{Color}}{ name of color for system }
#'   \item{\code{r}}{ red value for system }
#'   \item{\code{g}}{ green value for system }
#'   \item{\code{b}}{ blue value for system }
#'   \item{\code{Anatomy}}{ anatomical location as 
#'   determined by OASIS labeling }
#'   \item{\code{Lobe}}{ lobe location of node }
#'   \item{\code{Brodmann}}{ Broadmann area number }
#'   \item{\code{AAL}}{ AAL region label }
#' }
#' #' @references \url{http://www.nil.wustl.edu/labs/petersen/Resources.html}
#' 
#' @examples 
#' data(powers_areal_mni_itk)
#' \dontrun{
#'   fixed <- antsImageRead( getANTsRData("ch2") )
#'   moving <- antsImageRead( getANTsRData("mni") )
#'   mytx <- antsRegistration( fixed=fixed, moving=moving, 
#'   typeofTransform = c("SyN") )
#'   data( "powers_areal_mni_itk", package = "ANTsR", envir = environment() )
#'   coords = powers_areal_mni_itk[,1:3]
#'   ch2reg   = antsRegistration( fixed, moving, typeofTransform = "SyN" )
#'   coordsw <- antsApplyTransformsToPoints( 
#'   dim=3, points=coords,
#'   transformlist=ch2reg$fwdtransforms,
#'   whichtoinvert=c(FALSE,FALSE) )
#'   ptrd = 3
#'   powersLabels = makePointsImage( coordsw, moving, radius = pard )
#'   plot( moving, powersLabels, axis=3, nslices=30 )
#' }
#' @keywords datasets
"powers_areal_mni_itk"


#' @title tracts
#' @docType data
#' @description A data frame label numbers and names for 
#' the white matter tracts labels.
#' @format A data frame listing the following variables.
#' \describe{
#' \item{\code{label_num}}{ Numerical label value. } 
#' \item{\code{label_name}}{ Shorthand anatomical value. }
#' }
#' @references \url{http://www.ncbi.nlm.nih.gov/pubmed/18407524}
#' @examples data(tracts)
#' @keywords datasets
"tracts"


#' @title AAL Labels
#' @docType data
#' @description A data frame label numbers and names 
#' for the neuroanatomical AAL labels.
#' @format A data frame listing the following variables.
#' \describe{
#'   \item{\code{label_num}}{ Numerical label value. }
#'   \item{\code{label_name}}{ Shorthand anatomical value. }
#'   \item{\code{cerebellum}}{binary value}
#'   \item{\code{cortex}}{binary value}
#'   \item{\code{deepgrey}}{binary value}
#'   \item{\code{frontal}}{binary value}
#'   \item{\code{isdmn}}{binary value}
#'   \item{\code{issalience}}{binary value}
#'   \item{\code{left}}{binary value}
#'   \item{\code{limbic}}{binary value}
#'   \item{\code{occipital}}{binary value}
#'   \item{\code{parietal}}{binary value}
#'   \item{\code{right}}{binary value}
#'   \item{\code{temporal}}{binary value}
#'   \item{\code{unknown}}{binary value}
#' }
#' @references 
#' \url{http://en.wikipedia.org/wiki/Automated_Anatomical_Labeling}
#' @examples 
#' data(aal)
#' @keywords datasets
"aal"


#' @name antsrVersions
#' @title antsrVersions
#' @docType data
#' @description A data frame defining the git tag 
#' for the current ANTsR version.  One can also see 
#' antsrVersions from ANTsRCore to get the git tag for 
#' those dependencies.
#' @format   A data frame listing the following variables.
#' \describe{
#'   \item{\code{Dependency}}{ Name of software dependency. }
#'   \item{\code{GitTag}}{ The git tag.  This can also be used to 
#'   trace other dependencies, e.g. the ITK version used by the 
#'   current ANTs version. }
#' }
#' @references \url{https://github.com/stnava/ANTs}
#' @examples data(antsrVersions)
#' @keywords datasets
NULL