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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

891

Version

1.33.0

License

GPL-2

Maintainer

John Muschelli

Last Published

July 23rd, 2025

Functions in neurobase (1.33.0)

checkniigz-methods

Force object to filename with .nii.gz extension

Change Data type for img

copyNIfTIHeader

Copy NIfTI Header to an array

Image Center of Gravity

Add a colorbar to an ortho2 object

Perform Cut on an image

Density of Values in an Image

Calculate Dice from a Table

dropEmptyImageDimensions

Drop Empty Image Dimensions

Double Orthographic Display

emptyImageDimensionsMask

Make Mask from Empty Image Dimensions

getEmptyImageDimensions

Get Empty Image Dimensions

Ensure an array output

Get Image file extension

Fast Dice Tabulation

finite_img-methods

Histogram of Values in an Image

Flip NifTI Image

Transform set of images to matrix

Reading NIfTI images through RNifti

Image Time Series to list

Image Time Series to Data.frame

Mean of Values in an Image

Convert Image to Data.frame with Colors

img_ts_to_matrix

Image Time Series to Matrix

Image List to Time Series

Retrieve Image Indices

maskEmptyImageDimensions-methods

Apply Masking from Empty Image Dimensions

Extract or Replace Values Inside a Mask

Sample Quantiles

Parse Image Extensions

minmax_img-methods

Normalize Image using Range

Reorient an Image to RPI orientation

Plot differences for Prediction and Gold Standard

Make new nifti from array

Resets image parameters for a copied nifti object

Create Quantile Image

Orthographic Display, added options

Read NIfTI file reoriented to RPI

Grab nii file stubname

readNIfTI with default non-reorientation

Create Multi-Image Plot with Overlays

replaceEmptyImageDimensions-methods

Replace Subsetting from Empty Image Dimensions

Remake Image from Vector

Create Random `nifti` object

Randomize Image based on Mask

replace_dropped_dimensions

Remake Dropped Dimensions

Build Filename (usually for images)

replace_outside_surface

Replace Values Outside Surface of image

nifti image windower

subset_dti-methods

Subset DTI data based on b-values #'

Check if Objects have Same Dimensions

Window image based on quantiles of Image

Create temporary nii.gz file

reverse_orient_rpi

Reverse Reorientation an Image to RPI orientation

slice_colour_df

Slice a Image Color Data.frame

separate_img-methods

Separate Labeled Image into Multiple Binary Images

Get Z-score over a margin of an img

writeNIfTI with default non-reorientation

Zero pads an image

General NIfTI Writer

Image Center of Gravity Wrapper

Find Image z-limits

check_nifti_header-methods

Check if nifti image or read in a nifti header

applyEmptyImageDimensions-methods

Apply Subsetting from Empty Image Dimensions

Find Breaks for nifti Image Plotting

checknii-methods

Force object to filename with .nii extension

check_mask_fail

Check Mask is Binary, Fail otherwise

check_nifti-methods

Check if nifti image or read in a nifti image

Check Mask is Binary

Boxplot of Values in an Image

checkimg-methods

Force object to filename

Check output filename