# 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

## Documentation for package ‘neurobase’ version 1.13.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

applyEmptyImageDimensions | Apply Subsetting from Empty Image Dimensions
apply_empty_dim | Apply Subsetting from Empty Image Dimensions
boxplot.anlz | Boxplot of Values in an Image
boxplot.nifti | Boxplot of Values in an Image
breaker | Find Breaks for nifti Image Ploting
checkimg | Force object to filename
checkimg-method | Force object to filename
checkimg-methods | Force object to filename
checknii | Force object to filename with .nii extension
checknii-method | Force object to filename with .nii extension
checknii-methods | Force object to filename with .nii extension
checkniigz | Force object to filename with .nii.gz extension
checkniigz-method | Force object to filename with .nii.gz extension
checkniigz-methods | Force object to filename with .nii.gz extension
check_mask | Check Mask is Binary
check_mask_fail | Check Mask is Binary, Fail otherwise
check_nifti | Check if nifti image or read in a nifti image
check_nifti-method | Check if nifti image or read in a nifti image
check_nifti-methods | Check if nifti image or read in a nifti image
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
datatyper | Change Data type for img
density.anlz | Density of Values in an Image
density.nifti | Density of Values in an Image
double_ortho | Double Orthographic Display
dropEmptyImageDimensions | Drop Empty Image Dimensions
drop_empty_dim | Drop Empty Image Dimensions
ensure_nii | Force object to filename with .nii extension
ensure_nii_gz | Force object to filename with .nii.gz extension
fast_readnii | Reading NIfTI images through RNifti
file_imgext | Get Image file extension
finite_img | Finite Image
finite_img-method | Finite Image
finite_img-methods | Finite Image
getEmptyImageDimensions | Get Empty Image Dimensions
get_empty_dim | Get Empty Image Dimensions
hist.anlz | Histogram of Values in an Image
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_empty_dim | Make Mask from Empty Image Dimensions
mask_img | Mask nifti Image
mask_vals | Extract or Replace Values Inside a Mask
mask_vals-methods, | Extract or Replace Values Inside a Mask
mask_vals<- | Extract or Replace Values Inside a Mask
mask_vals<--method | Extract or Replace Values Inside a Mask
mean.anlz | Mean of Values in an Image
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.anlz | Sample Quantiles
quantile.nifti | Sample Quantiles
quantile_img | Create Quantile Image
randomize_mask | Randomize Image based on Mask
readNIfTI2 | readNIfTI with default non-reorientation
readnii | 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
writenii | 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