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

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 publication2017-01-06 10:11:56
MaintainerJohn Muschelli <muschellij2@gmail.com>
LicenseGPL-2
Version1.9.2

View on CRAN

Man pages

applyEmptyImageDimensions: Apply Subsetting from Empty Image Dimensions

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

replace_dropped_dimensions: Remake Dropped Dimensions

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

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

Files

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

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