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#' ciftiTools: Tools for Reading and Visualizing CIFTI Brain Files
#'
#' Here are groups of commonly-used functions in \code{ciftiTools}:
#'
#' Functions for reading in CIFTI or GIFTI data:
#'
#' \describe{
#' \item{\code{read_xifti}:}{ Read in a CIFTI file as a \code{"xifti"}}
#' \item{\code{read_xifti2}:}{ Read in GIFTI files as a \code{"xifti"}}
#' \item{\code{as.xifti}:}{ Combine numeric data to form a \code{"xifti"}}
#' \item{\code{read_surf}:}{ Read in a surface GIFTI file as a \code{"surf"}}
#' \item{\code{info_cifti}:}{ Read the metadata in a CIFTI file}
#' \item{\code{load_surf}:}{ Read in a surface included in \code{ciftiTools}}
#' \item{\code{load_parc}:}{ Read in a parcellation included in \code{ciftiTools}}
#' }
#'
#' Functions for writing CIFTI or GIFTI data:
#'
#' \describe{
#' \item{\code{write_cifti}:}{ Write a \code{"xifti"} to a CIFTI file}
#' \item{\code{write_xifti2}:}{ Write a \code{"xifti"} to GIFTI and NIFTI files}
#' \item{\code{write_metric_gifti}:}{ Write a numeric data matrix to a metric GIFTI file}
#' \item{\code{write_surf_gifti}:}{ Write a \code{"surf"} to a surface GIFTI file}
#' \item{\code{write_subcort_nifti}:}{ Write subcortical data to NIFTI files}
#' \item{\code{separate_cifti}:}{ Separate a CIFTI file into GIFTI and NIFTI files}
#' }
#'
#' Functions for manipulating \code{"xifti"}s:
#'
#' \describe{
#' \item{\code{apply_xifti}:}{ Apply a function along the rows or columns of the \code{"xifti"} data matrix}
#' \item{\code{combine_xifti}:}{ Combine multiple \code{"xifti"}s with non-overlapping brain structures}
#' \item{\code{convert_xifti}:}{ Convert the intent of a \code{"xifti"}}
#' \item{\code{merge_xifti}:}{ Concatenate data matrices from multiple \code{"xifti"}s}
#' \item{\code{newdata_xifti}:}{ Replace the data matrix in a \code{"xifti"}}
#' \item{\code{remove_xifti}:}{ Remove a brain structure or surface from a \code{"xifti"}}
#' \item{\code{select_xifti}:}{ Select data matrix columns of a \code{"xifti"}}
#' \item{\code{transform_xifti}:}{ Apply a univariate transformation to a \code{"xifti"} or pair of \code{"xifti"}s}
#' \item{\code{add_surf}:}{ Add surfaces to a \code{"xifti"}}
#' \item{\code{move_from_mwall}:}{ Move medial wall vertices back into the \code{"xifti"} data matrix}
#' \item{\code{move_to_mwall}:}{ Move rows with a certain value into the \code{"xifti"} medial wall mask}
#' }
#'
#' S3 methods for \code{"xifti"}s:
#'
#' \describe{
#' \item{\code{summary} and \code{print}:}{ Summarize the contents.}
#' \item{\code{as.matrix}:}{ Convert data to a locations by measurements numeric matrix.}
#' \item{\code{dim}:}{ Obtain number of locations and number of measurements.}
#' \item{\code{plot}:}{ Visualize the cortical surface and/or subcortical data.}
#' \item{\code{+}, \code{-}, \code{*}, \code{/}, \code{^}, \code{\%\%}, \code{\%/\%}:}{ Operation between a \code{"xifti"} and a scalar, or between two \code{"xifti"}s.}
#' \item{\code{abs}, \code{ceiling}, \code{exp}, \code{floor}, \code{log}, \code{round}, \code{sign}, and \code{sqrt}:}{ Univariate transformation of \code{"xifti"} data.}
#' }
#'
#' Functions for working with surfaces:
#'
#' \describe{
#' \item{\code{read_surf}:}{ Read in a surface GIFTI file as a \code{"surf"}}
#' \item{\code{is.surf}:}{ Verify a \code{"surf"}}
#' \item{\code{write_surf_gifti}:}{ Write a \code{"surf"} to a surface GIFTI file}
#' \item{\code{view_surf}:}{ Visualize a \code{"surf"}}
#' \item{\code{resample_surf}:}{ Resample a \code{"surf"}}
#' \item{\code{rotate_surf}:}{ Rotate the geometry of a \code{"surf"}}
#' }
#'
#' @name ciftiTools
"_PACKAGE"
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