#' @name readFileList
#' @title A function for reading a list of T1 volumetric mricloud data
#' @param fileList a vector of file names, passed to \code{\link{readSubjectDf}}
#' @param idList an optional list of ids, otherwise is 1 : length(fileList)
#' @param fixT2 optional, should the target2.img rawid errors
#' be fixed (for older images)
#' @param fixBF optional, should basalForebrain mislabeling be
#' fixed (for older images)
#' @description A function for reading in a collection of files of
#' T1 volumetric output
#' from MRIcloud. The files must be a list of files
#' @importFrom magrittr "%>%"
#' @importFrom dplyr filter mutate
#' @export
readFileList = function(fileList, idList = NULL, fixT2 = FALSE, fixBF = FALSE){
if (is.null(idList)) idList = 1 : length(fileList)
else if (length(idList) != length(fileList)) {
stop("idList and fileList must have equal length")
}
## read in each file, convert to data frame,
## add icv and tbv and id variable
lapply(1 : length(fileList), function(i) {
## Take the file and read it in
f = fileList[i] %>%
readSubjectDf()
## If required, fix the basaForebrain and
## target2 errors
if (fixT2) f = f %>% fixTarget2()
if (fixBF) f = f %>% fixBasalForebrain()
## Finish reading it in
f %>%
mutate(id = idList[i]) %>%
addSubjectICV() %>%
addSubjectTBV()
}
) %>% do.call(what = "rbind") #convert to data frame
}
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