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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

730

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 of Values in an Image

Change Data type for img

Perform Cut on an image

Fast Dice Tabulation

Histogram of Values in an Image

Convert Image to Data.frame with Colors

dropEmptyImageDimensions

Drop Empty Image Dimensions

emptyImageDimensionsMask

Make Mask from Empty Image Dimensions

Retrieve Image Indices

Ensure an array output

maskEmptyImageDimensions-methods

Apply Masking from Empty Image Dimensions

Parse Image Extensions

Reorient an Image to RPI orientation

finite_img-methods

Mean of Values in an Image

Grab nii file stubname

Get Image file extension

Extract or Replace Values Inside a Mask

Create Random `nifti` object

Reading NIfTI images through RNifti

Create Quantile Image

Make new nifti from array

Resets image parameters for a copied nifti object

getEmptyImageDimensions

Get Empty Image Dimensions

Flip NifTI Image

slice_colour_df

Slice a Image Color Data.frame

Sample Quantiles

replaceEmptyImageDimensions-methods

Replace Subsetting from Empty Image Dimensions

separate_img-methods

Separate Labeled Image into Multiple Binary Images

Build Filename (usually for images)

replace_dropped_dimensions

Remake Dropped Dimensions

Image Time Series to list

replace_outside_surface

Replace Values Outside Surface of image

Image List to Time Series

Randomize Image based on Mask

readNIfTI with default non-reorientation

nifti image windower

Plot differences for Prediction and Gold Standard

Transform set of images to matrix

Image Time Series to Data.frame

Orthographic Display, added options

Find Image z-limits

img_ts_to_matrix

Image Time Series to Matrix

Create Multi-Image Plot with Overlays

Zero pads an image

Read NIfTI file reoriented to RPI

reverse_orient_rpi

Reverse Reorientation an Image to RPI orientation

Remake Image from Vector

minmax_img-methods

Normalize Image using Range

subset_dti-methods

Subset DTI data based on b-values #'

writeNIfTI with default non-reorientation

Get Z-score over a margin of an img

Create temporary nii.gz file

General NIfTI Writer

Image Center of Gravity Wrapper

Window image based on quantiles of Image

Check if Objects have Same Dimensions

check_mask_fail

Check Mask is Binary, Fail otherwise

Find Breaks for nifti Image Plotting

check_nifti-methods

Check if nifti image or read in a nifti image

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 output filename

checknii-methods

Force object to filename with .nii extension

applyEmptyImageDimensions-methods

Apply Subsetting from Empty Image Dimensions

Check Mask is Binary

Add a colorbar to an ortho2 object

copyNIfTIHeader

Copy NIfTI Header to an array

Double Orthographic Display

Calculate Dice from a Table

Image Center of Gravity