R/reg_whitestripe.R
In muschellij2/extrantsr: Extra Functions to Build on the 'ANTsR' Package
Defines functions
reg_whitestripe
Documented in
reg_whitestripe
#' @title WhiteStripe Normalization
#'
#' @description This function performs registration to a T1 template
#' using ANTsR and SyN transformation
#' @param t1 filename (or nifti objects) of T1 image
#' @param t2 filename (or nifti objects) of T2 image
#' @param register Register image to template file
#' @param native If images are registered, should the native space
#' normalized image be returned?
#' @param template.file Filename of template to warp to
#' @param typeofTransform type of transformed used, passed to
#' \code{\link{antsRegistration}}
#' @param interpolator Interpolation to be performed, passed to
#' \code{\link{antsRegistration}}
#' @param type Type of whitestripe normalization done
#' @param t1.outfile Output filename of normalized T1 image
#' @param t2.outfile Output filename of normalized T2 image
#' @param other.files Character filenames or list of nifti objects to
#' normalize. In the same space as T1.
#' @param other.outfiles Character filenames for output
#' normalized files.
#' @param ws.outfile Character filename for output
#' whitestripe mask.
#' @param mask File or nifti image of brain mask
#' @param mask.outfile Character filename for output
#' brain mask.
#' @param verbose Print Diagnostic Messages
#' @param reproducible Sets the seed and
#' \code{Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 1)}.
#' See
#' \url{https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues}
#' for discussion.
#' @param seed will execute
#' \code{Sys.setenv(ANTS_RANDOM_SEED = seed)} before
#' running to attempt a more reproducible result. If \code{NULL}, will not set anything,
#' but \code{reproducible} must be \code{FALSE}.
#' @param ... arguments to \code{\link{whitestripe}} or
#' \code{\link{whitestripe_hybrid}}
#' @export
#' @return List of nifti objects or character filenames
#' @importFrom fslr fsldir fslmask
#' @importFrom WhiteStripe whitestripe whitestripe_hybrid whitestripe_norm
#' @importFrom ANTsRCore antsImageRead antsImageClone
#' @importFrom oro.nifti cal_img writeNIfTI
reg_whitestripe <- function(
t1 =NULL, t2 = NULL,
register = TRUE,
native = TRUE,
template.file = file.path(fsldir(),
"data",
"standard",
paste0("MNI152_T1_1mm",
ifelse(is.null(mask), "",
"_brain"),
".nii.gz")),
typeofTransform = c("Rigid", "Affine"),
interpolator = "LanczosWindowedSinc",
type = c("T1", "T2", "hybrid"),
t1.outfile = NULL,
t2.outfile = NULL,
other.files = NULL,
other.outfiles = NULL,
ws.outfile = NULL,
mask = NULL,
mask.outfile = NULL,
verbose = TRUE,
reproducible = TRUE,
seed = 1,
...
){
#####################
# Checking for T1 and T2 iamges
#####################
typeofTransform = match.arg(typeofTransform, c("Rigid", "Affine"))
type = match.arg(type, c("T1", "T2", "hybrid"))
#####################
# Checking for T1 and T2 iamges
#####################
nullt1 = is.null(t1)
nullt2 = is.null(t2)
if (nullt1 & nullt2){
stop("Need a T1 or T2 image")
}
####################
# WhiteStripe file
####################
nullws = is.null(ws.outfile)
if (nullws){
ws.outfile = tempfile(fileext = ".nii.gz")
}
nullmask = is.null(mask)
nullmask.outfile = is.null(mask.outfile)
#####################
# Creating output mask
#####################
if (!nullmask){
if (verbose){
message("# Doing Checks on Mask \n")
}
# reading in T1
mask = checkimg(mask)
if (nullmask.outfile){
mask.outfile = tempfile(fileext = ".nii.gz")
}
mm = ANTsRCore::antsImageRead(filename = mask, dimension = 3)
maskants = ANTsRCore::antsImageClone(mm)
##################
# Must have extension
##################
# if (!all(grepl("[.]nii", c(mask.outfile)))){
# stop("t1 outfile must be nifti .nii or .nii.gz")
# }
}
#####################
# Creating output files
#####################
if (!nullt1){
#############
# Mask the images
###########
if (verbose){
message("# Doing Checks on T1 \n")
}
if (!nullmask){
tfile = tempfile()
fslmask(file = t1, mask = mask,
outfile = tfile, verbose = verbose)
ext = get.imgext()
t1 = paste0(tfile, ext)
rm(list="tfile")
}
# reading in T1
t1 = checkimg(t1)
if (is.null(t1.outfile)){
if (type %in% c("T1", "hybrid")){
stop("T1 outfile needs te specified if T1 specified")
} else {
t1.outfile = tempfile(fileext = ".nii.gz")
}
}
t1.outfile = path.expand(t1.outfile)
t1ants = ANTsRCore::antsImageRead(filename = t1, dimension = 3)
##################
# Must have extension
##################
if (!all(grepl("[.]nii", c(t1.outfile)))){
stop("t1 outfile must be nifti .nii or .nii.gz")
}
}
if (!nullt2){
#############
# Mask the images
###########
if (verbose){
message("# Doing Checks on T2 \n")
}
if (!nullmask){
tfile = tempfile()
fslmask(file = t2, mask = mask,
outfile = tfile, verbose = verbose)
ext = get.imgext()
t2 = paste0(tfile, ext)
rm(list="tfile")
}
# reading in T2
t2 = checkimg(t2)
if (is.null(t2.outfile)){
stop("T2 outfile needs te specified if T2 specified")
}
t2.outfile = path.expand(t2.outfile)
t2ants = ANTsRCore::antsImageRead(filename = t2, dimension = 3)
##################
# Must have extension
##################
if (!all(grepl("[.]nii", c(t2.outfile)))){
stop("t2 outfile must be nifti .nii or .nii.gz")
}
}
nullother = is.null(other.files)
if (!nullother){
stopifnot(length(other.files)== length(other.outfiles))
##################
# Must have extension
##################
if (!all(grepl("[.]nii", c(other.outfiles)))){
stop("All filenames must be nifti .nii or .nii.gz")
}
#############
# Mask the images
###########
if (verbose){
message("# Doing Checks on Other files \n")
}
if (!nullmask){
other.files = sapply(other.files, function(fname){
tfile = tempfile()
fslmask(file = fname, mask = mask, outfile = tfile, verbose = verbose)
ext = get.imgext()
tfile = paste0(tfile, ext)
return(tfile)
})
}
other.files = sapply(other.files, checkimg)
other.ants = lapply(other.files, function(x){
ANTsRCore::antsImageRead(filename = x, dimension = 3)
})
}
##### everything filesnames from here
###################
# Perform Registration
###################
if (register){
if (!nullother){
other.temp = sapply(seq(other.files),
function(x) tempfile(fileext = '.nii.gz'))
} else {
other.temp = NULL
}
outprefix = tempfile()
if (!nullt1){
###################
# Carry T2 with transformation
###################
if (!nullt2){
other.files = c(t2 = t2,
other.files)
other.temp = c(t2 = tempfile(fileext = '.nii.gz'),
other.temp)
}
###################
# Carry Mask with transformation
###################
if (!nullmask){
other.files = c(other.files, mask = mask)
other.temp = c(other.temp, mask = mask.outfile)
}
###################
# Register
###################
if (verbose){
message("# Registering to Template \n")
}
outfile = tempfile(fileext = '.nii.gz')
ants_regwrite(filename = t1,
retimg = FALSE,
outfile = outfile,
template.file = template.file,
typeofTransform = typeofTransform,
interpolator = interpolator,
outprefix = outprefix,
remove.warp = TRUE,
other.files = other.files,
other.outfiles = other.temp,
verbose = verbose)
t1 = check_nifti(outfile)
if (!nullt2){
t2 = other.temp[1]
t2 = check_nifti(t2)
other.temp = other.temp[-1]
other.files = other.files[-1]
}
if (!nullmask){
mask = other.temp[length(other.temp)]
mask = cal_img(check_nifti(mask) > 0.5)
other.temp = other.temp[-length(other.temp)]
other.files = other.files[-length(other.temp)]
}
if (!nullother){
other.files = lapply(other.temp, check_nifti)
}
} else {
stop("Registration must be done with the T1 image")
}
}
if (!nullt1){
t1 = check_nifti(t1)
}
if (!nullt2){
t2 = check_nifti(t2)
}
if (!nullmask){
mask = cal_img(check_nifti(mask) > 0.5)
}
if (!nullother){
other.files = lapply(other.files, check_nifti)
}
########### everything is images from here on out
###################
# Different Scenarios
###################
if (verbose){
message("# Running WhiteStripe Estimation \n")
}
if (type == "T1"){
if (!nullt2){
stop(paste0("T2 should not be specified when type = ",
"'T1', put in other.files"))
}
ws = whitestripe( t1, type = "T1", ...)
}
if (type == "T2"){
if (!nullt1){
if (!register){
stop(paste0("T1 should not be specified when type = ",
"'T2', put in other.files"))
}
}
ws = whitestripe( t2, type = "T2", ...)
}
if (type == "hybrid"){
ws = whitestripe_hybrid( t1 = t1, t2 = t2, ...)
}
##########################
# Get whitestripe indices
##########################
indices = ws$whitestripe.ind
mask.img = ws$mask.img
dtype = function(img){
img = drop_img_dim(img)
img = datatyper(img,
datatype= convert.datatype()$FLOAT32,
bitpix= convert.bitpix()$FLOAT32)
return(img)
}
##########################
# Apply WhiteStripe
##########################
if (verbose){
message("# Running WhiteStripe Normalization\n")
}
if (!nullt1){
t1 = dtype(whitestripe_norm(t1, indices = indices))
}
if (!nullt2){
t2 = dtype(whitestripe_norm(t2, indices = indices))
}
if (!nullother){
other.files = lapply(other.files, function(x){
dtype(whitestripe_norm(x, indices = indices))
})
}
###################
# Perform Registration
###################
if (native){
if (verbose){
message("# Returning images to Native Space\n")
}
# if (!register){
# warning(paste0("Native is TRUE, but register is FALSE,",
# "returning out images"))
# }
if (register){
inv.trans = paste0(outprefix, "0GenericAffine.mat")
template.img = antsImageRead(template.file, dimension = 3)
if (!nullt1){
##############################
# Applying Transformation
##############################
fixed = oro2ants(t1)
fixed = antsApplyTransforms(fixed = t1ants,
moving = fixed,
transformlist = inv.trans,
interpolator = interpolator,
whichtoinvert = 1)
t1 = ants2oro(fixed)
if (!nullws){
fixed = oro2ants(mask.img)
fixed = antsApplyTransforms(fixed = t1ants,
moving = fixed,
transformlist = inv.trans,
interpolator = interpolator,
whichtoinvert = 1)
mask.img = cal_img(ants2oro(fixed) > 0.5)
}
###################
# Carry T2 with transformation
###################
if (!nullt2){
fixed = oro2ants(t2)
fixed = antsApplyTransforms(fixed = t2ants,
moving = fixed,
transformlist = inv.trans,
interpolator = interpolator,
whichtoinvert = 1)
t2 = ants2oro(fixed)
}
###################
# Use Native mask Image
###################
if (!nullmask){
mask = ants2oro(maskants)
}
###################
# Register
###################
if (!nullother){
for (ifile in seq_along(other.files)){
fixed = oro2ants(other.files[[ifile]])
aimg = other.ants[[ifile]]
fixed = antsApplyTransforms(fixed = aimg,
moving = fixed,
transformlist = inv.trans,
interpolator = interpolator,
whichtoinvert = 1)
other.files[[ifile]] = ants2oro(fixed)
}
}
} else {
stop("Registration must be done with the T1 image")
}
}
}
###################
# Write out images
###################
if (verbose){
message("# Writing out Normalized Images\n")
}
if (!nullt1){
if (verbose){
message("# Writing out Normalized T1\n")
}
t1 = cal_img(t1)
t1 = mask_img(t1, mask)
writeNIfTI(t1, filename = nii.stub(t1.outfile))
}
if (!nullt2){
if (verbose){
message("# Writing out Normalized T2\n")
}
t2 = cal_img(t2)
t2 = mask_img(t2, mask)
writeNIfTI(t2, filename = nii.stub(t2.outfile))
}
if (!nullother){
if (verbose){
message("# Writing out Normalized Other Files\n")
}
print(other.outfiles)
mapply(function(img, fname){
img = cal_img(img)
img = mask_img(img, mask)
writeNIfTI(img, filename = nii.stub(fname))
}, other.files, other.outfiles)
}
if (!nullws){
if (verbose){
message("# Writing out WhiteStripe Mask\n")
}
mask.img = cal_img(mask.img)
writeNIfTI(mask.img, filename = nii.stub(ws.outfile))
} else {
mask.img = NULL
}
if (!nullmask.outfile){
if (verbose){
message("# Writing out Brain Mask Outfile\n")
}
mask = cal_img(mask)
writeNIfTI(mask, filename = nii.stub(mask.outfile))
}
return(list(t1 = t1,
t2 = t2,
other.files = other.files,
mask.img = mask.img,
native = native,
register = register,
ws.type = type
# template.file = template.file
))
}
muschellij2/extrantsr documentation built on July 27, 2021, 7:41 a.m.
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Defines functions reg_whitestripe
Documented in reg_whitestripe
#' @title WhiteStripe Normalization
#'
#' @description This function performs registration to a T1 template
#' using ANTsR and SyN transformation
#' @param t1 filename (or nifti objects) of T1 image
#' @param t2 filename (or nifti objects) of T2 image
#' @param register Register image to template file
#' @param native If images are registered, should the native space
#' normalized image be returned?
#' @param template.file Filename of template to warp to
#' @param typeofTransform type of transformed used, passed to
#' \code{\link{antsRegistration}}
#' @param interpolator Interpolation to be performed, passed to
#' \code{\link{antsRegistration}}
#' @param type Type of whitestripe normalization done
#' @param t1.outfile Output filename of normalized T1 image
#' @param t2.outfile Output filename of normalized T2 image
#' @param other.files Character filenames or list of nifti objects to
#' normalize. In the same space as T1.
#' @param other.outfiles Character filenames for output
#' normalized files.
#' @param ws.outfile Character filename for output
#' whitestripe mask.
#' @param mask File or nifti image of brain mask
#' @param mask.outfile Character filename for output
#' brain mask.
#' @param verbose Print Diagnostic Messages
#' @param reproducible Sets the seed and
#' \code{Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 1)}.
#' See
#' \url{https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues}
#' for discussion.
#' @param seed will execute
#' \code{Sys.setenv(ANTS_RANDOM_SEED = seed)} before
#' running to attempt a more reproducible result. If \code{NULL}, will not set anything,
#' but \code{reproducible} must be \code{FALSE}.
#' @param ... arguments to \code{\link{whitestripe}} or
#' \code{\link{whitestripe_hybrid}}
#' @export
#' @return List of nifti objects or character filenames
#' @importFrom fslr fsldir fslmask
#' @importFrom WhiteStripe whitestripe whitestripe_hybrid whitestripe_norm
#' @importFrom ANTsRCore antsImageRead antsImageClone
#' @importFrom oro.nifti cal_img writeNIfTI
reg_whitestripe <- function(
t1 =NULL, t2 = NULL,
register = TRUE,
native = TRUE,
template.file = file.path(fsldir(),
"data",
"standard",
paste0("MNI152_T1_1mm",
ifelse(is.null(mask), "",
"_brain"),
".nii.gz")),
typeofTransform = c("Rigid", "Affine"),
interpolator = "LanczosWindowedSinc",
type = c("T1", "T2", "hybrid"),
t1.outfile = NULL,
t2.outfile = NULL,
other.files = NULL,
other.outfiles = NULL,
ws.outfile = NULL,
mask = NULL,
mask.outfile = NULL,
verbose = TRUE,
reproducible = TRUE,
seed = 1,
...
){
#####################
# Checking for T1 and T2 iamges
#####################
typeofTransform = match.arg(typeofTransform, c("Rigid", "Affine"))
type = match.arg(type, c("T1", "T2", "hybrid"))
#####################
# Checking for T1 and T2 iamges
#####################
nullt1 = is.null(t1)
nullt2 = is.null(t2)
if (nullt1 & nullt2){
stop("Need a T1 or T2 image")
}
####################
# WhiteStripe file
####################
nullws = is.null(ws.outfile)
if (nullws){
ws.outfile = tempfile(fileext = ".nii.gz")
}
nullmask = is.null(mask)
nullmask.outfile = is.null(mask.outfile)
#####################
# Creating output mask
#####################
if (!nullmask){
if (verbose){
message("# Doing Checks on Mask \n")
}
# reading in T1
mask = checkimg(mask)
if (nullmask.outfile){
mask.outfile = tempfile(fileext = ".nii.gz")
}
mm = ANTsRCore::antsImageRead(filename = mask, dimension = 3)
maskants = ANTsRCore::antsImageClone(mm)
##################
# Must have extension
##################
# if (!all(grepl("[.]nii", c(mask.outfile)))){
# stop("t1 outfile must be nifti .nii or .nii.gz")
# }
}
#####################
# Creating output files
#####################
if (!nullt1){
#############
# Mask the images
###########
if (verbose){
message("# Doing Checks on T1 \n")
}
if (!nullmask){
tfile = tempfile()
fslmask(file = t1, mask = mask,
outfile = tfile, verbose = verbose)
ext = get.imgext()
t1 = paste0(tfile, ext)
rm(list="tfile")
}
# reading in T1
t1 = checkimg(t1)
if (is.null(t1.outfile)){
if (type %in% c("T1", "hybrid")){
stop("T1 outfile needs te specified if T1 specified")
} else {
t1.outfile = tempfile(fileext = ".nii.gz")
}
}
t1.outfile = path.expand(t1.outfile)
t1ants = ANTsRCore::antsImageRead(filename = t1, dimension = 3)
##################
# Must have extension
##################
if (!all(grepl("[.]nii", c(t1.outfile)))){
stop("t1 outfile must be nifti .nii or .nii.gz")
}
}
if (!nullt2){
#############
# Mask the images
###########
if (verbose){
message("# Doing Checks on T2 \n")
}
if (!nullmask){
tfile = tempfile()
fslmask(file = t2, mask = mask,
outfile = tfile, verbose = verbose)
ext = get.imgext()
t2 = paste0(tfile, ext)
rm(list="tfile")
}
# reading in T2
t2 = checkimg(t2)
if (is.null(t2.outfile)){
stop("T2 outfile needs te specified if T2 specified")
}
t2.outfile = path.expand(t2.outfile)
t2ants = ANTsRCore::antsImageRead(filename = t2, dimension = 3)
##################
# Must have extension
##################
if (!all(grepl("[.]nii", c(t2.outfile)))){
stop("t2 outfile must be nifti .nii or .nii.gz")
}
}
nullother = is.null(other.files)
if (!nullother){
stopifnot(length(other.files)== length(other.outfiles))
##################
# Must have extension
##################
if (!all(grepl("[.]nii", c(other.outfiles)))){
stop("All filenames must be nifti .nii or .nii.gz")
}
#############
# Mask the images
###########
if (verbose){
message("# Doing Checks on Other files \n")
}
if (!nullmask){
other.files = sapply(other.files, function(fname){
tfile = tempfile()
fslmask(file = fname, mask = mask, outfile = tfile, verbose = verbose)
ext = get.imgext()
tfile = paste0(tfile, ext)
return(tfile)
})
}
other.files = sapply(other.files, checkimg)
other.ants = lapply(other.files, function(x){
ANTsRCore::antsImageRead(filename = x, dimension = 3)
})
}
##### everything filesnames from here
###################
# Perform Registration
###################
if (register){
if (!nullother){
other.temp = sapply(seq(other.files),
function(x) tempfile(fileext = '.nii.gz'))
} else {
other.temp = NULL
}
outprefix = tempfile()
if (!nullt1){
###################
# Carry T2 with transformation
###################
if (!nullt2){
other.files = c(t2 = t2,
other.files)
other.temp = c(t2 = tempfile(fileext = '.nii.gz'),
other.temp)
}
###################
# Carry Mask with transformation
###################
if (!nullmask){
other.files = c(other.files, mask = mask)
other.temp = c(other.temp, mask = mask.outfile)
}
###################
# Register
###################
if (verbose){
message("# Registering to Template \n")
}
outfile = tempfile(fileext = '.nii.gz')
ants_regwrite(filename = t1,
retimg = FALSE,
outfile = outfile,
template.file = template.file,
typeofTransform = typeofTransform,
interpolator = interpolator,
outprefix = outprefix,
remove.warp = TRUE,
other.files = other.files,
other.outfiles = other.temp,
verbose = verbose)
t1 = check_nifti(outfile)
if (!nullt2){
t2 = other.temp[1]
t2 = check_nifti(t2)
other.temp = other.temp[-1]
other.files = other.files[-1]
}
if (!nullmask){
mask = other.temp[length(other.temp)]
mask = cal_img(check_nifti(mask) > 0.5)
other.temp = other.temp[-length(other.temp)]
other.files = other.files[-length(other.temp)]
}
if (!nullother){
other.files = lapply(other.temp, check_nifti)
}
} else {
stop("Registration must be done with the T1 image")
}
}
if (!nullt1){
t1 = check_nifti(t1)
}
if (!nullt2){
t2 = check_nifti(t2)
}
if (!nullmask){
mask = cal_img(check_nifti(mask) > 0.5)
}
if (!nullother){
other.files = lapply(other.files, check_nifti)
}
########### everything is images from here on out
###################
# Different Scenarios
###################
if (verbose){
message("# Running WhiteStripe Estimation \n")
}
if (type == "T1"){
if (!nullt2){
stop(paste0("T2 should not be specified when type = ",
"'T1', put in other.files"))
}
ws = whitestripe( t1, type = "T1", ...)
}
if (type == "T2"){
if (!nullt1){
if (!register){
stop(paste0("T1 should not be specified when type = ",
"'T2', put in other.files"))
}
}
ws = whitestripe( t2, type = "T2", ...)
}
if (type == "hybrid"){
ws = whitestripe_hybrid( t1 = t1, t2 = t2, ...)
}
##########################
# Get whitestripe indices
##########################
indices = ws$whitestripe.ind
mask.img = ws$mask.img
dtype = function(img){
img = drop_img_dim(img)
img = datatyper(img,
datatype= convert.datatype()$FLOAT32,
bitpix= convert.bitpix()$FLOAT32)
return(img)
}
##########################
# Apply WhiteStripe
##########################
if (verbose){
message("# Running WhiteStripe Normalization\n")
}
if (!nullt1){
t1 = dtype(whitestripe_norm(t1, indices = indices))
}
if (!nullt2){
t2 = dtype(whitestripe_norm(t2, indices = indices))
}
if (!nullother){
other.files = lapply(other.files, function(x){
dtype(whitestripe_norm(x, indices = indices))
})
}
###################
# Perform Registration
###################
if (native){
if (verbose){
message("# Returning images to Native Space\n")
}
# if (!register){
# warning(paste0("Native is TRUE, but register is FALSE,",
# "returning out images"))
# }
if (register){
inv.trans = paste0(outprefix, "0GenericAffine.mat")
template.img = antsImageRead(template.file, dimension = 3)
if (!nullt1){
##############################
# Applying Transformation
##############################
fixed = oro2ants(t1)
fixed = antsApplyTransforms(fixed = t1ants,
moving = fixed,
transformlist = inv.trans,
interpolator = interpolator,
whichtoinvert = 1)
t1 = ants2oro(fixed)
if (!nullws){
fixed = oro2ants(mask.img)
fixed = antsApplyTransforms(fixed = t1ants,
moving = fixed,
transformlist = inv.trans,
interpolator = interpolator,
whichtoinvert = 1)
mask.img = cal_img(ants2oro(fixed) > 0.5)
}
###################
# Carry T2 with transformation
###################
if (!nullt2){
fixed = oro2ants(t2)
fixed = antsApplyTransforms(fixed = t2ants,
moving = fixed,
transformlist = inv.trans,
interpolator = interpolator,
whichtoinvert = 1)
t2 = ants2oro(fixed)
}
###################
# Use Native mask Image
###################
if (!nullmask){
mask = ants2oro(maskants)
}
###################
# Register
###################
if (!nullother){
for (ifile in seq_along(other.files)){
fixed = oro2ants(other.files[[ifile]])
aimg = other.ants[[ifile]]
fixed = antsApplyTransforms(fixed = aimg,
moving = fixed,
transformlist = inv.trans,
interpolator = interpolator,
whichtoinvert = 1)
other.files[[ifile]] = ants2oro(fixed)
}
}
} else {
stop("Registration must be done with the T1 image")
}
}
}
###################
# Write out images
###################
if (verbose){
message("# Writing out Normalized Images\n")
}
if (!nullt1){
if (verbose){
message("# Writing out Normalized T1\n")
}
t1 = cal_img(t1)
t1 = mask_img(t1, mask)
writeNIfTI(t1, filename = nii.stub(t1.outfile))
}
if (!nullt2){
if (verbose){
message("# Writing out Normalized T2\n")
}
t2 = cal_img(t2)
t2 = mask_img(t2, mask)
writeNIfTI(t2, filename = nii.stub(t2.outfile))
}
if (!nullother){
if (verbose){
message("# Writing out Normalized Other Files\n")
}
print(other.outfiles)
mapply(function(img, fname){
img = cal_img(img)
img = mask_img(img, mask)
writeNIfTI(img, filename = nii.stub(fname))
}, other.files, other.outfiles)
}
if (!nullws){
if (verbose){
message("# Writing out WhiteStripe Mask\n")
}
mask.img = cal_img(mask.img)
writeNIfTI(mask.img, filename = nii.stub(ws.outfile))
} else {
mask.img = NULL
}
if (!nullmask.outfile){
if (verbose){
message("# Writing out Brain Mask Outfile\n")
}
mask = cal_img(mask)
writeNIfTI(mask, filename = nii.stub(mask.outfile))
}
return(list(t1 = t1,
t2 = t2,
other.files = other.files,
mask.img = mask.img,
native = native,
register = register,
ws.type = type
# template.file = template.file
))
}
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