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neurobase

'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.

Functions (75)

applyEmptyImageDimensions-methods

Apply Subsetting from Empty Image Dimensions

boxplot.nifti

Boxplot of Values in an Image

breaker

Find Breaks for nifti Image Plotting

check_mask

Check Mask is Binary

check_mask_fail

Check Mask is Binary, Fail otherwise

check_nifti-methods

Check if nifti image or read in a nifti image

check_nifti_header-methods

Check if nifti image or read in a nifti header

check_outfile

Check output filename

checkimg-methods

Force object to filename

checknii-methods

Force object to filename with .nii extension

checkniigz-methods

Force object to filename with .nii.gz extension

cog

Image Center of Gravity

colorbar

Add a colorbar to an ortho2 object

copyNIfTIHeader

Copy NIfTI Header to an array

cut.nifti

Perform Cut on an image

datatype

Change Data type for img

density.nifti

Density of Values in an Image

dicer

Calculate Dice from a Table

double_ortho

Double Orthographic Display

dropEmptyImageDimensions

Drop Empty Image Dimensions

emptyImageDimensionsMask

Make Mask from Empty Image Dimensions

ensure_array

Ensure an array output

fast_dice_tab

Fast Dice Tabulation

fast_readnii

Reading NIfTI images through RNifti

file_imgext

Get Image file extension

finite_img-methods

Finite Image

flip_img

Flip NifTI Image

getEmptyImageDimensions

Get Empty Image Dimensions

hist.nifti

Histogram of Values in an Image

images2matrix

Transform set of images to matrix

img_colour_df

Convert Image to Data.frame with Colors

img_indices

Retrieve Image Indices

img_list_to_ts

Image List to Time Series

img_ts_to_df

Image Time Series to Data.frame

img_ts_to_list

Image Time Series to list

img_ts_to_matrix

Image Time Series to Matrix

maskEmptyImageDimensions-methods

Apply Masking from Empty Image Dimensions

mask_img

Mask Image

mask_vals-methods

Extract or Replace Values Inside a Mask

mean.nifti

Mean of Values in an Image

minmax_img-methods

Normalize Image using Range

multi_overlay

Create Multi-Image Plot with Overlays

newnii

Resets image parameters for a copied nifti object

niftiarr

Make new nifti from array

nii.stub

Grab nii file stubname

orient_rpi

Reorient an Image to RPI orientation

ortho2

Orthographic Display, added options

ortho_diff

Plot differences for Prediction and Gold Standard

parse_img_ext

Parse Image Extensions

quantile.nifti

Sample Quantiles

quantile_img

Create Quantile Image

random_nifti

Create Random 'nifti' object

randomize_mask

Randomize Image based on Mask

readNIfTI2

readNIfTI with default non-reorientation

read_rpi

Read NIfTI file reoriented to RPI

remake_img

Remake Image from Vector

remap_filename

Build Filename (usually for images)

replaceEmptyImageDimensions-methods

Replace Subsetting from Empty Image Dimensions

replace_dropped_dimensions

Remake Dropped Dimensions

replace_outside_surface

Replace Values Outside Surface of image

rescale_img

Image Rescaler

reverse_orient_rpi

Reverse Reorientation an Image to RPI orientation

robust_window

Window image based on quantiles of Image

same_dims

Check if Objects have Same Dimensions

separate_img-methods

Separate Labeled Image into Multiple Binary Images

slice_colour_df

Slice a Image Color Data.frame

subset_dti-methods

Subset DTI data based on b-values #'

tempimg

Create temporary nii.gz file

window_img

nifti image windower

writeNIfTI2

writeNIfTI with default non-reorientation

write_nifti

General NIfTI Writer

xyz

Image Center of Gravity Wrapper

zero_pad

Zero pads an image

zlimmer

Find Image z-limits

zscore_img

Get Z-score over a margin of an img

neurobase

'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

v1.32.1

GPL-2

Authors

John Muschelli [aut, cre]

Initial release

neurobase

Functions (75)

neurobase

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