neurobase: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects
Version 1.13.2

Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.

AuthorJohn Muschelli <muschellij2@gmail.com>
Date of publication2017-03-03 21:25:51
MaintainerJohn Muschelli <muschellij2@gmail.com>
LicenseGPL-2
Version1.13.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("neurobase")

Getting started

NIfTI Basics
Sending Messages With Gmailr

Popular man pages

checkimg-methods: Force object to filename
checkniigz-methods: Force object to filename with .nii.gz extension
mask_img: Mask nifti Image
multi_overlay: Create Multi-Image Plot with Overlays
niftiarr: Make new nifti from array
replace_outside_surface: Replace Values Outside Surface of image
zero_pad: Zero pads an image
See all...

All man pages Function index File listing

Man pages

applyEmptyImageDimensions: Apply Subsetting from Empty Image Dimensions
boxplot.nifti: Boxplot of Values in an Image
breaker: Find Breaks for nifti Image Ploting
checkimg-methods: Force object to filename
check_mask: Check Mask is Binary
check_mask_fail: Check Mask is Binary, Fail otherwise
check_nifti-methods: Check if nifti image or read in a nifti image
checkniigz-methods: Force object to filename with .nii.gz extension
checknii-methods: Force object to filename with .nii extension
check_outfile: Check output filename
cog: Image Center of Gravity
colorbar: Add a colorbar to an ortho2 object
copyNIfTIHeader: Copy NIfTI Header to an array
datatype: Change Data type for img
density.nifti: Density of Values in an Image
double_ortho: Double Orthographic Display
dropEmptyImageDimensions: Drop Empty Image Dimensions
fast_readnii: Reading NIfTI images through RNifti
file_imgext: Get Image file extension
finite_img-methods: Finite Image
getEmptyImageDimensions: Get Empty Image Dimensions
hist.nifti: Histogram of Values in an Image
images2matrix: Transform set of images to matrix
img_indices: Retrieve Image Indices
maskEmptyImageDimensions: Make Mask from Empty Image Dimensions
mask_img: Mask nifti Image
mask_vals-methods: Extract or Replace Values Inside a Mask
mean.nifti: Mean of Values in an Image
multi_overlay: Create Multi-Image Plot with Overlays
newnii: Resets image parameters for a copied nifti object
niftiarr: Make new nifti from array
nii.stub: Grab nii file stubname
ortho2: Orthographic Display, added options
ortho_diff: Plot differences for Prediction and Gold Standard
parse_img_ext: Parse Image Extensions
quantile_img: Create Quantile Image
quantile.nifti: Sample Quantiles
randomize_mask: Randomize Image based on Mask
readNIfTI2: readNIfTI with default non-reorientation
remake_img: Remake Image from Vector
remap_filename: Build Filename (usually for images)
replace_dropped_dimensions: Remake Dropped Dimensions
replace_outside_surface: Replace Values Outside Surface of image
rescale_img: Image Rescaler
robust_window: Window image based on quantiles of Image
same_dims: Check if Objects have Same Dimensions
tempimg: Create temporary nii.gz file
window_img: nifti image windower
writeNIfTI2: writeNIfTI with default non-reoirientation
xyz: Image Center of Gravity Wrapper
zero_pad: Zero pads an image
zlimmer: Find Image z-limits
zscore_img: Get Z-score over a margin of an img

Functions

applyEmptyImageDimensions Man page Source code
apply_empty_dim Man page Source code
boxplot.anlz Man page Source code
boxplot.nifti Man page Source code
breaker Man page Source code
cal_mask_vals Source code
check_mask Man page Source code
check_mask_fail Man page Source code
check_nifti Man page
check_nifti,ANY-method Man page
check_nifti,anlz-method Man page
check_nifti,array-method Man page
check_nifti,character-method Man page
check_nifti,factor-method Man page
check_nifti,list-method Man page
check_nifti,nifti-method Man page
check_nifti-methods Man page
check_outfile Man page Source code
checkimg Man page
checkimg,ANY-method Man page
checkimg,character-method Man page
checkimg,list-method Man page
checkimg,nifti-method Man page
checkimg-methods Man page
checknii Man page
checknii,ANY-method Man page
checknii,character-method Man page
checknii,list-method Man page
checknii,nifti-method Man page
checknii-methods Man page
checkniigz Man page
checkniigz,ANY-method Man page
checkniigz,character-method Man page
checkniigz,list-method Man page
checkniigz,nifti-method Man page
checkniigz-methods Man page
cog Man page Source code
colorbar Man page Source code
copyNIfTIHeader Man page Source code
datatype Man page
datatyper Man page Source code
density.anlz Man page Source code
density.nifti Man page Source code
double_ortho Man page Source code
dropEmptyImageDimensions Man page Source code
drop_empty_dim Man page Source code
ensure_nii Man page Source code
ensure_nii_gz Man page Source code
fast_readnii Man page Source code
file_imgext Man page Source code
finite_img Man page
finite_img,ANY-method Man page
finite_img,character-method Man page
finite_img,list-method Man page
finite_img,nifti-method Man page
finite_img-methods Man page
getEmptyImageDimensions Man page Source code
get_empty_dim Man page Source code
hist.anlz Man page Source code
hist.nifti Man page Source code
images2matrix Man page Source code
img_indices Man page Source code
maskEmptyImageDimensions Man page Source code
mask_empty_dim Man page Source code
mask_img Man page Source code
mask_vals Man page Source code Source code
mask_vals-methods, Man page
mask_vals<- Man page
mask_vals<-,anlz,ANY,ANY-method Man page
mask_vals<-,anlz-method Man page
mask_vals<-,array,ANY,ANY-method Man page
mask_vals<-,array-method Man page
mask_vals<-,nifti,ANY,ANY-method Man page
mask_vals<-,nifti-method Man page
mean.anlz Man page Source code
mean.nifti Man page Source code
multi_overlay Man page Source code
newnii Man page Source code
niftiarr Man page Source code
nii.stub Man page Source code
ortho2 Man page Source code
ortho_diff Man page Source code
parse_img_ext Man page Source code
quantile.anlz Man page Source code
quantile.nifti Man page Source code
quantile_img Man page Source code
quick_check Source code
randomize_mask Man page Source code
readNIfTI2 Man page Source code
readnii Man page Source code
remake_img Man page Source code
remap_filename Man page Source code
replace_dropped_dimensions Man page Source code
replace_outside_surface Man page Source code
rescale_img Man page Source code
robust_window Man page Source code
same_dims Man page Source code
tempimg Man page Source code
window_img Man page Source code
writeNIfTI2 Man page Source code
writenii Man page Source code
xyz Man page Source code
zero_pad Man page Source code
zlimmer Man page Source code
zscore_img Man page Source code

Files

inst
inst/doc
inst/doc/nifti_basics.html
inst/doc/neurobase.html
inst/doc/neurobase.Rmd
inst/doc/nifti_basics.Rmd
inst/doc/neurobase.R
inst/doc/nifti_basics.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test-finite_img.R
tests/testthat/test-file_imgext.R
tests/testthat/test-datatyper.R
tests/testthat/test-mask_img.R
tests/testthat/test-cog.R
tests/testthat/test-breaker.R
tests/testthat/test-check_mask.R
tests/testthat/test-checknii.R
tests/testthat/test-drop_apply_dims.R
tests/testthat/test-randomize_mask.R
tests/testthat/test-check_outfile.R
tests/testthat/test-checkimg.R
NAMESPACE
R
R/rescale_img.R
R/writenii.R
R/replace_dropped_dimensions.R
R/tempimg.R
R/quantile.nifti.R
R/zlimmer.R
R/remake_img.R
R/check_outfile.R
R/check_nifti.R
R/quantile_img.R
R/double_ortho.R
R/nii.stub.R
R/readNIfTI2.R
R/niftiarr.R
R/fast_readnii.R
R/zero_pad.R
R/remap_filename.R
R/checkniigz.R
R/mask_vals.R
R/window_img.R
R/dropEmptyImageDimensions.R
R/mask_img.R
R/density.nifti.R
R/file_imgext.R
R/img_indices.R
R/maskEmptyImageDimensions.R
R/check_mask.R
R/boxplot.nifti.R
R/ortho_diff.R
R/import_methods.R
R/applyEmptyImageDimensions.R
R/checknii.R
R/breaker.R
R/checkimg.R
R/overlay2.R
R/cog.R
R/copyNIfTIHeader.R
R/replace_outside_hull.R
R/robust_window.R
R/hist.nifti.R
R/images2matrix.R
R/ortho2.R
R/getEmptyImageDimensions.R
R/randomize_mask.R
R/same_dims.R
R/mean.nifti.R
R/parse_img_ext.R
R/finite_img.R
vignettes
vignettes/neurobase.Rmd
vignettes/nifti_basics.Rmd
vignettes/nifti_basics_cache
vignettes/nifti_basics_cache/html
vignettes/nifti_basics_cache/html/make_dists_0ac09f4fbac80b1c5dc89493d412b811.rdx
vignettes/nifti_basics_cache/html/make_dists_0ac09f4fbac80b1c5dc89493d412b811.RData
vignettes/nifti_basics_cache/html/__packages
vignettes/nifti_basics_cache/html/make_dists_0ac09f4fbac80b1c5dc89493d412b811.rdb
vignettes/nifti_basics_files
vignettes/nifti_basics_files/figure-html
vignettes/nifti_basics_files/figure-html/ortho2_large-1.png
vignettes/nifti_basics_files/figure-html/dens_2-1.png
vignettes/nifti_basics_files/figure-html/double_ortho-1.png
vignettes/nifti_basics_files/figure-html/ortho2_nona-1.png
vignettes/nifti_basics_files/figure-html/plot_mask-1.png
vignettes/nifti_basics_files/figure-html/dens-1.png
vignettes/nifti_basics_files/figure-html/ortho2_zlim-1.png
vignettes/nifti_basics_files/figure-html/ortho2_rob-1.png
vignettes/nifti_basics_files/figure-html/one_slice-1.png
vignettes/nifti_basics_files/figure-html/make_dists-1.png
vignettes/nifti_basics_files/figure-html/all_slices-1.png
vignettes/nifti_basics_files/figure-html/plot_red-1.png
vignettes/nifti_basics_files/figure-html/one_slice_sag-1.png
vignettes/nifti_basics_files/figure-html/one_slice_overlay_right-1.png
vignettes/nifti_basics_files/figure-html/ortho2_noorient-1.png
vignettes/nifti_basics_files/figure-html/two_slice-1.png
vignettes/nifti_basics_files/figure-html/ortho2-1.png
vignettes/nifti_basics_files/figure-html/ortho-1.png
vignettes/nifti_basics_files/figure-html/one_slice_overlay-1.png
vignettes/nifti_basics_files/figure-html/ortho_nona-1.png
vignettes/nifti_basics_files/figure-html/plot_full_eve-1.png
vignettes/nifti_basics_files/figure-html/make_hex-1.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/checkniigz-methods.Rd
man/copyNIfTIHeader.Rd
man/datatype.Rd
man/writeNIfTI2.Rd
man/img_indices.Rd
man/check_mask_fail.Rd
man/hist.nifti.Rd
man/density.nifti.Rd
man/mask_img.Rd
man/file_imgext.Rd
man/ortho2.Rd
man/mean.nifti.Rd
man/window_img.Rd
man/zscore_img.Rd
man/remap_filename.Rd
man/mask_vals-methods.Rd
man/tempimg.Rd
man/quantile.nifti.Rd
man/niftiarr.Rd
man/ortho_diff.Rd
man/remake_img.Rd
man/cog.Rd
man/zlimmer.Rd
man/readNIfTI2.Rd
man/quantile_img.Rd
man/check_mask.Rd
man/parse_img_ext.Rd
man/zero_pad.Rd
man/randomize_mask.Rd
man/replace_outside_surface.Rd
man/rescale_img.Rd
man/double_ortho.Rd
man/newnii.Rd
man/maskEmptyImageDimensions.Rd
man/dropEmptyImageDimensions.Rd
man/fast_readnii.Rd
man/breaker.Rd
man/xyz.Rd
man/multi_overlay.Rd
man/applyEmptyImageDimensions.Rd
man/finite_img-methods.Rd
man/colorbar.Rd
man/check_nifti-methods.Rd
man/getEmptyImageDimensions.Rd
man/robust_window.Rd
man/check_outfile.Rd
man/boxplot.nifti.Rd
man/replace_dropped_dimensions.Rd
man/nii.stub.Rd
man/checkimg-methods.Rd
man/checknii-methods.Rd
man/same_dims.Rd
man/images2matrix.Rd
neurobase documentation built on May 20, 2017, 2:09 a.m.

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