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

## Documentation for package ‘neurobase’ version 1.34.0

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

## Help Pages

A B C D E F G H I M N O P Q R S T W X Z

## -- A --

applyEmptyImageDimensions | Apply Subsetting from Empty Image Dimensions
applyEmptyImageDimensions-method | Apply Subsetting from Empty Image Dimensions
applyEmptyImageDimensions-methods | Apply Subsetting from Empty Image Dimensions
apply_empty_dim | Apply Subsetting from Empty Image Dimensions

## -- B --

boxplot.anlz | Boxplot of Values in an Image
boxplot.nifti | Boxplot of Values in an Image
breaker | Find Breaks for nifti Image Plotting

## -- C --

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_nifti_header | Check if nifti image or read in a nifti header
check_nifti_header-method | Check if nifti image or read in a nifti header
check_nifti_header-methods | Check if nifti image or read in a nifti header
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
cut.anlz | Perform Cut on an image
cut.nifti | Perform Cut on an image

## -- D --

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
dicer | Calculate Dice from a Table
double_ortho | Double Orthographic Display
dropEmptyImageDimensions | Drop Empty Image Dimensions
drop_empty_dim | Drop Empty Image Dimensions

## -- E --

emptyImageDimensionsMask | Make Mask from Empty Image Dimensions
empty_dim_mask | Make Mask from Empty Image Dimensions
ensure_array | Ensure an array output
ensure_nii | Force object to filename with .nii extension
ensure_nii_gz | Force object to filename with .nii.gz extension

## -- F --

fast_dice | Fast Dice Tabulation
fast_dice_tab | Fast Dice Tabulation
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
flip_img | Flip NIfTI Image

## -- G --

getEmptyImageDimensions | Get Empty Image Dimensions
get_empty_dim | Get Empty Image Dimensions

## -- H --

hist.anlz | Histogram of Values in an Image
hist.nifti | Histogram of Values in an Image

## -- I --

images2matrix | Transform set of images to matrix
img_color_df | Convert Image to Data.frame with Colors
img_colour_df | Convert Image to Data.frame with Colors
img_indices | Retrieve Image Indices
img_list_to_ts | Image List to Time Series
img_ts_to_df | Image Time Series to Data.frame
img_ts_to_list | Image Time Series to list
img_ts_to_matrix | Image Time Series to Matrix
is_rpi_oriented | Reorient an Image to RPI orientation

## -- M --

maskEmptyImageDimensions | Apply Masking from Empty Image Dimensions
maskEmptyImageDimensions-method | Apply Masking from Empty Image Dimensions
maskEmptyImageDimensions-methods | Apply Masking from Empty Image Dimensions
mask_empty_dim | Apply Masking from Empty Image Dimensions
mask_img | Mask 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
minmax_img | Normalize Image using Range
minmax_img-method | Normalize Image using Range
minmax_img-methods | Normalize Image using Range
multi_overlay | Create Multi-Image Plot with Overlays
multi_overlay_center | Create Multi-Image Plot with Overlays
multi_overlay_diff | Plot differences for Prediction and Gold Standard

## -- N --

newnii | Resets image parameters for a copied nifti object
niftiarr | Make new nifti from array
nii.stub | Grab nii file stubname

## -- O --

orient_rpi | Reorient an Image to RPI orientation
orient_rpi_file | Reorient an Image to RPI orientation
ortho2 | Orthographic Display, added options
ortho_diff | Plot differences for Prediction and Gold Standard

## -- P --

parse_img_ext | Parse Image Extensions

## -- Q --

quantile.anlz | Sample Quantiles
quantile.nifti | Sample Quantiles
quantile_img | Create Quantile Image

## -- R --

randomize_mask | Randomize Image based on Mask
random_nifti | Create Random 'nifti' object
readNIfTI2 | readNIfTI with default non-reorientation
readnii | readNIfTI with default non-reorientation
read_rpi | Read NIfTI file reoriented to RPI
remake_img | Remake Image from Vector
remap_filename | Build Filename (usually for images)
replaceEmptyImageDimensions | Replace Subsetting from Empty Image Dimensions
replaceEmptyImageDimensions-method | Replace Subsetting from Empty Image Dimensions
replaceEmptyImageDimensions-methods | Replace Subsetting from Empty Image Dimensions
replace_dropped_dimensions | Remake Dropped Dimensions
replace_empty_dim | Replace Subsetting from Empty Image Dimensions
replace_outside_surface | Replace Values Outside Surface of image
rescale_img | Image Rescaler
reverse_orient_rpi | Reverse Reorientation an Image to RPI orientation
reverse_orient_rpi_file | Reverse Reorientation an Image to RPI orientation
robust_window | Window image based on quantiles of Image

## -- S --

same_dims | Check if Objects have Same Dimensions
separate_img | Separate Labeled Image into Multiple Binary Images
separate_img-method | Separate Labeled Image into Multiple Binary Images
separate_img-methods | Separate Labeled Image into Multiple Binary Images
slice_colour_df | Slice a Image Color Data.frame
subset_dti | Subset DTI data based on b-values #'
subset_dti-method | Subset DTI data based on b-values #'
subset_dti-methods | Subset DTI data based on b-values #'

## -- T --

tempimg | Create temporary nii.gz file

## -- W --

window_img | nifti image windower
writeNIfTI2 | writeNIfTI with default non-reorientation
writenii | writeNIfTI with default non-reorientation
write_nifti | General NIfTI Writer

## -- X --

xyz | Image Center of Gravity Wrapper

## -- Z --

zero_pad | Zero pads an image
zlimmer | Find Image z-limits
zscore_img | Get Z-score over a margin of an img