diff --git a/.Rbuildignore b/.Rbuildignore
index d4e3ba1..9e21e23 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,4 @@
+^\.Rhistory$
 ^Doxyfile$
 ^\.travis\.yml$
 ^.*\.Rproj$
diff --git a/.Rhistory b/.Rhistory
deleted file mode 100644
index 807a535..0000000
--- a/.Rhistory
+++ /dev/null
@@ -1,512 +0,0 @@
-rm(list=ls())
-nifti = c("sizeof_hdr", "data_type", "db_name", "extents",
-"session_error", "regular", "dim_info", "dim_",
-"intent_p1", "intent_p2", "intent_p3", "intent_code",
-"datatype", "bitpix", "slice_start", "pixdim",
-"vox_offset", "scl_slope", "scl_inter", "slice_end",
-"slice_code", "xyzt_units", "cal_max", "cal_min",
-"slice_duration", "toffset", "glmax", "glmin",
-"descrip", "aux_file", "qform_code", "sform_code",
-"quatern_b", "quatern_c", "quatern_d", "qoffset_x",
-"qoffset_y", "qoffset_z", "srow_x", "srow_y", "srow_z",
-"intent_name", "magic", "extender", ".Data")
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package="RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-img = readNIfTI(fname)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-hdr_names
-hdr_off
-img_off
-setdiff(hdr_names, img_names)
-hdr$dim
-rm(list=ls())
-nifti = c("sizeof_hdr", "data_type", "db_name", "extents",
-"session_error", "regular", "dim_info", "dim_",
-"intent_p1", "intent_p2", "intent_p3", "intent_code",
-"datatype", "bitpix", "slice_start", "pixdim",
-"vox_offset", "scl_slope", "scl_inter", "slice_end",
-"slice_code", "xyzt_units", "cal_max", "cal_min",
-"slice_duration", "toffset", "glmax", "glmin",
-"descrip", "aux_file", "qform_code", "sform_code",
-"quatern_b", "quatern_c", "quatern_d", "qoffset_x",
-"qoffset_y", "qoffset_z", "srow_x", "srow_y", "srow_z",
-"intent_name", "magic", "extender", ".Data")
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package="RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = readNIfTI(fname)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-setdiff(hdr_names, img_names)
-rm(list=ls())
-nifti = c("sizeof_hdr", "data_type", "db_name", "extents",
-"session_error", "regular", "dim_info", "dim_",
-"intent_p1", "intent_p2", "intent_p3", "intent_code",
-"datatype", "bitpix", "slice_start", "pixdim",
-"vox_offset", "scl_slope", "scl_inter", "slice_end",
-"slice_code", "xyzt_units", "cal_max", "cal_min",
-"slice_duration", "toffset", "glmax", "glmin",
-"descrip", "aux_file", "qform_code", "sform_code",
-"quatern_b", "quatern_c", "quatern_d", "qoffset_x",
-"qoffset_y", "qoffset_z", "srow_x", "srow_y", "srow_z",
-"intent_name", "magic", "extender", ".Data")
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package="RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = readNIfTI(fname)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-add = setdiff(img_names, hdr_names)
-add
-img@datatype
-img@data_type
-rm(list=ls())
-library(oro.nifti)
-# options(error = quote(print("Error Ocurred")))
-URL <- "http://imaging.mrc-cbu.cam.ac.uk/downloads/Colin/colin_1mm.tgz"
-urlfile <- file.path("~/Desktop/scratch/", "colin_1mm.tgz")
-# if (!file.exists(urlfile)){
-download.file(URL, dest=urlfile, quiet=TRUE)
-untar(urlfile, exdir=path.expand("~/Desktop/scratch/"))
-# }
-img <- readNIfTI(file.path("~/Desktop/scratch/", "colin_1mm"), verbose=TRUE)
-# img_corr <- readNIfTI(file.path("~/Desktop/scratch/", "ncolin_1mm"),
-#                       verbose=TRUE)
-readNifti(file.path("~/Desktop/scratch/", "colin_1mm"))
-image =readNifti(file.path("~/Desktop/scratch/", "colin_1mm"))
-writeNifti(image, file = tempfile(fileext = ".nii.gz"))
-?nifti
-rm(list=ls())
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = readNIfTI(fname)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-add = setdiff(img_names, hdr_names)
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-# rnii2oro = function(image) {
-arr = as(image, "array")
-hdr = dumpNifti(image)
-dtype = hdr$datatype
-hdr$reorient = FALSE
-img = nifti(arr)
-#######################################
-# Get the names
-#######################################
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-#######################################
-# Stop if these have changed
-#######################################
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-#######################################
-# See where they both work
-#######################################
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-add = setdiff(img_names, hdr_names)
-add
-img@session_error
-rm(list=ls())
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = readNIfTI(fname)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-add = setdiff(img_names, hdr_names)
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-# rnii2oro = function(image) {
-arr = as(image, "array")
-hdr = dumpNifti(image)
-dtype = hdr$datatype
-hdr$reoriented = FALSE
-img = nifti(arr)
-#######################################
-# Get the names
-#######################################
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-#######################################
-# Stop if these have changed
-#######################################
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-#######################################
-# See where they both work
-#######################################
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-#######################################
-#
-#######################################
-add = setdiff(img_names, hdr_names)
-# }
-add
-img@reoriented
-img_off
-rm(list=ls())
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = readNIfTI(fname)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-add = setdiff(img_names, hdr_names)
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-# rnii2oro = function(image) {
-arr = as(image, "array")
-hdr = dumpNifti(image)
-dtype = hdr$datatype
-img = nifti(arr)
-#######################################
-# Get the names
-#######################################
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-#######################################
-# Stop if these have changed
-#######################################
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-#######################################
-# See where they both work
-#######################################
-both = intersect(img_names, hdr_names)
-#######################################
-#
-#######################################
-add = setdiff(img_names, hdr_names)
-for (islot in both) {
-slot(img, islot) = hdr[[islot]]
-}
-# }
-rm(list=ls())
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = readNIfTI(fname)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-add = setdiff(img_names, hdr_names)
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-img_off
-source('~/Desktop/fastnii.R')
-rm(list=ls())
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = readNIfTI(fname)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-add = setdiff(img_names, hdr_names)
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-# rnii2oro = function(image) {
-arr = as(image, "array")
-hdr = dumpNifti(image)
-dtype = hdr$datatype
-img = nifti(arr)
-#######################################
-# Get the names
-#######################################
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-#######################################
-# Stop if these have changed
-#######################################
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-wrong
-source('~/Desktop/fastnii.R')
-img
-writenii(img, filename = tempfile(fileext = ".nii.gz"))
-writeNIfTI(img, filename = tempfile(fileext = ".nii.gz"))
-class(image)
-library(RNifti)
-rm(list = ls())
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = readNIfTI(fname)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-add = setdiff(img_names, hdr_names)
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-img_off
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-img = oro.nifti::readNIfTI(fname)
-out = nii2oro(image)
-nii2oro
-arr = as(image, "array")
-hdr = dumpNifti(image)
-hdr_names = sort(names(hdr))
-stopifnot( !("dim_" %in% names(hdr)))
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = nifti(arr)
-img
-img_names = sort(slotNames(img))
-#######################################
-# Stop if these have changed
-# This means one of the standards have changed
-#######################################
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-wrong
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-img = oro.nifti::readNIfTI(fname)
-out = nii2oro(image)
-out
-all.equal(out, img)
-out@regular
-img@regular
-rm(list = ls())
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-hdr = dumpNifti(image)
-hdr$dim_ = hdr$dim
-hdr$dim = NULL
-img = readNIfTI(fname, reorient = FALSE)
-img_names = sort(slotNames(img))
-hdr_names = sort(names(hdr))
-wrong = setdiff(hdr_names, img_names)
-stopifnot(length(wrong) == 0)
-add = setdiff(img_names, hdr_names)
-both = intersect(img_names, hdr_names)
-hdr_vals = lapply(both, function(x){
-hdr[[x]]
-})
-img_vals = lapply(both, function(x){
-slot(img, x)
-})
-names(hdr_vals) = names(img_vals) = both
-check = mapply(function(x, y){
-all(x == y)
-}, hdr_vals, img_vals)
-img_off = img_vals[!check]
-hdr_off = hdr_vals[!check]
-img_off
-hdr_vals
-img_vals
-ig
-img
-out
-img@regular
-oro.nifti:::readNIfTI()
-oro.nifti:::readNIfTI
-oro.nifti::: .read.nifti.content
-img@datatype
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-img = oro.nifti::readNIfTI(fname, reorient = FALSE)
-out = nii2oro(image)
-all.equal(out)
-all.equal(out, img)
-nifti
-source('~/Desktop/fastnii.R')
-hdr$qform_code
-hdr$regular
-img@regular
-add = setdiff(img_names, hdr_names)
-add
-library(RNifti)
-library(oro.nifti)
-fname = system.file("extdata", "example.nii.gz", package = "RNifti")
-image <- readNifti(fname)
-img = oro.nifti::readNIfTI(fname, reorient = FALSE)
-out = nii2oro(image)
-all.equal(out, img)
-```
-out@bitpix
-image$bitpix
-out@bitpix
-out@datatype
-img@datatype
-img@bitpix
-fname
-fslhd(fname)
-library(fslr)
-fslhd(fname)
-fname
-fslhd(fname)[1:10]
-fslhd(fname)[c(1, 4, 11:20)]
-fslhd(fname)[c(1, 4, 15:17)]
-library(RNifti)
-?readNifti
-file = system.file("extdata", "example.nii.gz")
-is.niftiImage(file)
-img = readNifti(file)
-is.niftiImage(img)
-is.internalImage(img)
-int_img = readNifti(file, internal = TRUE)
-is.niftiImage(int_img)
-is.internalImage(int_img)