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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

810

Version

1.32.3

License

GPL-2

Maintainer

John Muschelli

Last Published

October 23rd, 2022

Functions in neurobase (1.32.3)

copyNIfTIHeader

Copy NIfTI Header to an array

Add a colorbar to an ortho2 object

Perform Cut on an image

Histogram of Values in an Image

Change Data type for img

Flip NifTI Image

getEmptyImageDimensions

Get Empty Image Dimensions

Double Orthographic Display

Get Image file extension

dropEmptyImageDimensions

Drop Empty Image Dimensions

Transform set of images to matrix

finite_img-methods

Fast Dice Tabulation

Reading NIfTI images through RNifti

Image List to Time Series

Ensure an array output

emptyImageDimensionsMask

Make Mask from Empty Image Dimensions

maskEmptyImageDimensions-methods

Apply Masking from Empty Image Dimensions

Retrieve Image Indices

Convert Image to Data.frame with Colors

Sample Quantiles

Parse Image Extensions

Plot differences for Prediction and Gold Standard

Orthographic Display, added options

Create Multi-Image Plot with Overlays

minmax_img-methods

Normalize Image using Range

Image Time Series to list

img_ts_to_matrix

Image Time Series to Matrix

Resets image parameters for a copied nifti object

Image Time Series to Data.frame

Make new nifti from array

Grab nii file stubname

Extract or Replace Values Inside a Mask

Reorient an Image to RPI orientation

Mean of Values in an Image

replace_dropped_dimensions

Remake Dropped Dimensions

Create Quantile Image

Create Random `nifti` object

Build Filename (usually for images)

Remake Image from Vector

Read NIfTI file reoriented to RPI

nifti image windower

writeNIfTI with default non-reorientation

replace_outside_surface

Replace Values Outside Surface of image

reverse_orient_rpi

Reverse Reorientation an Image to RPI orientation

Window image based on quantiles of Image

Check if Objects have Same Dimensions

General NIfTI Writer

subset_dti-methods

Subset DTI data based on b-values #'

replaceEmptyImageDimensions-methods

Replace Subsetting from Empty Image Dimensions

Create temporary nii.gz file

Image Center of Gravity Wrapper

Get Z-score over a margin of an img

Randomize Image based on Mask

readNIfTI with default non-reorientation

separate_img-methods

Separate Labeled Image into Multiple Binary Images

Find Image z-limits

slice_colour_df

Slice a Image Color Data.frame

Zero pads an image

checkimg-methods

Force object to filename

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 Mask is Binary

applyEmptyImageDimensions-methods

Apply Subsetting from Empty Image Dimensions

check_nifti-methods

Check if nifti image or read in a nifti image

Check output filename

Boxplot of Values in an Image

check_nifti_header-methods

Check if nifti image or read in a nifti header

Image Center of Gravity

Calculate Dice from a Table

checkniigz-methods

Force object to filename with .nii.gz extension

Density of Values in an Image