#' @rdname recon_manual
#' @aliases recon_con1,recon_con2,recon_con3
#' @title Reconstruction from Motion Correction to Skull Strip
#' @description Reconstruction from Freesurfer for Step 1-5
#' (Motion Correction to Skull Strip), which calls \code{-autorecon1}
#' in \code{recon-all}
#'
#' @note See https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all for the
#' steps of each \code{autorecon1-3}.
#' If you set \code{infile = NULL}, then you can omit the
#' \code{-i} flag in \code{recon-all}.
#' @param infile Input filename (dcm or nii)
#' @param outdir Output directory
#' @param subjid subject id
#' @param verbose print diagnostic messages
#'
#' @return Result of \code{\link{system}}
#' @export
recon_con1 <- function(
infile,
outdir = NULL,
subjid,
verbose = TRUE
) {
reconner(infile = infile,
outdir = outdir,
subjid = subjid,
verbose = verbose,
opts = "-autorecon1")
}
#' @rdname recon_manual
#' @export
autorecon1 <- function(
infile,
outdir = NULL,
subjid,
verbose = TRUE
) {
recon_con1(
infile = infile,
outdir = outdir,
subjid = subjid,
verbose = verbose)
}
#' @rdname recon_manual
#' @export
recon_con2 <- function(
infile,
outdir = NULL,
subjid,
verbose = TRUE
) {
reconner(infile = infile,
outdir = outdir,
subjid = subjid,
verbose = verbose,
opts = "-autorecon2")
}
#' @rdname recon_manual
#' @export
autorecon2 <- function(
infile,
outdir = NULL,
subjid,
verbose = TRUE
) {
recon_con2(
infile = infile,
outdir = outdir,
subjid = subjid,
verbose = verbose)
}
#' @rdname recon_manual
#' @export
recon_con3 <- function(
infile,
outdir = NULL,
subjid,
verbose = TRUE
) {
reconner(infile = infile,
outdir = outdir,
subjid = subjid,
verbose = verbose,
opts = "-autorecon3")
}
#' @rdname recon_manual
#' @export
autorecon3 <- function(
infile,
outdir = NULL,
subjid,
verbose = TRUE
) {
recon_con3(
infile = infile,
outdir = outdir,
subjid = subjid,
verbose = verbose)
}
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