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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

5,509

Version

1.34.0

License

GPL-2

Maintainer

John Muschelli

Last Published

October 17th, 2025

Functions in neurobase (1.34.0)

finite_img-methods

getEmptyImageDimensions

Get Empty Image Dimensions

Density of Values in an Image

Perform Cut on an image

dropEmptyImageDimensions

Drop Empty Image Dimensions

Transform set of images to matrix

Get Image file extension

Ensure an array output

Reading NIfTI images through RNifti

maskEmptyImageDimensions-methods

Apply Masking from Empty Image Dimensions

Extract or Replace Values Inside a Mask

img_ts_to_matrix

Image Time Series to Matrix

Image Time Series to list

Image Time Series to Data.frame

Image List to Time Series

Mean of Values in an Image

Retrieve Image Indices

Grab nii file stubname

Make new nifti from array

Convert Image to Data.frame with Colors

Orthographic Display, added options

Reorient an Image to RPI orientation

Create Multi-Image Plot with Overlays

minmax_img-methods

Normalize Image using Range

Plot differences for Prediction and Gold Standard

Create Quantile Image

Create Random `nifti` object

Parse Image Extensions

replace_outside_surface

Replace Values Outside Surface of image

Resets image parameters for a copied nifti object

replaceEmptyImageDimensions-methods

Replace Subsetting from Empty Image Dimensions

Build Filename (usually for images)

Sample Quantiles

Randomize Image based on Mask

readNIfTI with default non-reorientation

replace_dropped_dimensions

Remake Dropped Dimensions

slice_colour_df

Slice a Image Color Data.frame

separate_img-methods

Separate Labeled Image into Multiple Binary Images

nifti image windower

Check if Objects have Same Dimensions

General NIfTI Writer

Image Center of Gravity Wrapper

writeNIfTI with default non-reorientation

Get Z-score over a margin of an img

reverse_orient_rpi

Reverse Reorientation an Image to RPI orientation

Remake Image from Vector

Window image based on quantiles of Image

Read NIfTI file reoriented to RPI

Create temporary nii.gz file

subset_dti-methods

Subset DTI data based on b-values #'

Zero pads an image

Find Image z-limits

check_nifti_header-methods

Check if nifti image or read in a nifti header

check_mask_fail

Check Mask is Binary, Fail otherwise

Check output filename

applyEmptyImageDimensions-methods

Apply Subsetting from Empty Image Dimensions

checkimg-methods

Force object to filename

Boxplot of Values in an Image

Find Breaks for nifti Image Plotting

Check Mask is Binary

checkniigz-methods

Force object to filename with .nii.gz extension

check_nifti-methods

Check if nifti image or read in a nifti image

checknii-methods

Force object to filename with .nii extension

Add a colorbar to an ortho2 object

copyNIfTIHeader

Copy NIfTI Header to an array

Double Orthographic Display

Fast Dice Tabulation

Flip NIfTI Image

Calculate Dice from a Table

Change Data type for img

emptyImageDimensionsMask

Make Mask from Empty Image Dimensions

Image Center of Gravity

Histogram of Values in an Image