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neurobase

The goal of neurobase is to add functionality to oro.nifti and it is the baseline package for Neuroconductor.

Installation

You can install neurobase from github with:

# install.packages("devtools")
devtools::install_github("muschellij2/neurobase")

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Version

Install

install.packages('neurobase')

Monthly Downloads

719

Version

1.32.4

License

GPL-2

Maintainer

Last Published

May 9th, 2024

Functions in neurobase (1.32.4)

checkniigz-methods

Force object to filename with .nii.gz extension
density.nifti

Density of Values in an Image
datatype

Change Data type for img
cut.nifti

Perform Cut on an image
fast_dice_tab

Fast Dice Tabulation
hist.nifti

Histogram of Values in an Image
img_colour_df

Convert Image to Data.frame with Colors
dropEmptyImageDimensions

Drop Empty Image Dimensions
emptyImageDimensionsMask

Make Mask from Empty Image Dimensions
img_indices

Retrieve Image Indices
ensure_array

Ensure an array output
mask_img

Mask Image
maskEmptyImageDimensions-methods

Apply Masking from Empty Image Dimensions
parse_img_ext

Parse Image Extensions
orient_rpi

Reorient an Image to RPI orientation
finite_img-methods

Finite Image
mean.nifti

Mean of Values in an Image
nii.stub

Grab nii file stubname
file_imgext

Get Image file extension
mask_vals

Extract or Replace Values Inside a Mask
random_nifti

Create Random `nifti` object
fast_readnii

Reading NIfTI images through RNifti
quantile_img

Create Quantile Image
niftiarr

Make new nifti from array
newnii

Resets image parameters for a copied nifti object
getEmptyImageDimensions

Get Empty Image Dimensions
flip_img

Flip NifTI Image
slice_colour_df

Slice a Image Color Data.frame
quantile.nifti

Sample Quantiles
replaceEmptyImageDimensions-methods

Replace Subsetting from Empty Image Dimensions
separate_img-methods

Separate Labeled Image into Multiple Binary Images
remap_filename

Build Filename (usually for images)
replace_dropped_dimensions

Remake Dropped Dimensions
img_ts_to_list

Image Time Series to list
replace_outside_surface

Replace Values Outside Surface of image
img_list_to_ts

Image List to Time Series
randomize_mask

Randomize Image based on Mask
readNIfTI2

readNIfTI with default non-reorientation
window_img

nifti image windower
ortho_diff

Plot differences for Prediction and Gold Standard
images2matrix

Transform set of images to matrix
img_ts_to_df

Image Time Series to Data.frame
ortho2

Orthographic Display, added options
zlimmer

Find Image z-limits
img_ts_to_matrix

Image Time Series to Matrix
multi_overlay

Create Multi-Image Plot with Overlays
zero_pad

Zero pads an image
read_rpi

Read NIfTI file reoriented to RPI
rescale_img

Image Rescaler
reverse_orient_rpi

Reverse Reorientation an Image to RPI orientation
remake_img

Remake Image from Vector
minmax_img-methods

Normalize Image using Range
subset_dti-methods

Subset DTI data based on b-values #'
writeNIfTI2

writeNIfTI with default non-reorientation
zscore_img

Get Z-score over a margin of an img
tempimg

Create temporary nii.gz file
write_nifti

General NIfTI Writer
xyz

Image Center of Gravity Wrapper
robust_window

Window image based on quantiles of Image
same_dims

Check if Objects have Same Dimensions
check_mask_fail

Check Mask is Binary, Fail otherwise
breaker

Find Breaks for nifti Image Plotting
check_nifti-methods

Check if nifti image or read in a nifti image
boxplot.nifti

Boxplot of Values in an Image
check_nifti_header-methods

Check if nifti image or read in a nifti header
checkimg-methods

Force object to filename
check_outfile

Check output filename
checknii-methods

Force object to filename with .nii extension
applyEmptyImageDimensions-methods

Apply Subsetting from Empty Image Dimensions
check_mask

Check Mask is Binary
colorbar

Add a colorbar to an ortho2 object
copyNIfTIHeader

Copy NIfTI Header to an array
double_ortho

Double Orthographic Display
dicer

Calculate Dice from a Table
cog

Image Center of Gravity