getMask: Get Mask

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Get Mask

Description

Get a binary mask image from the given image after thresholding.

Usage

getMask(img, lowThresh, highThresh, cleanup = 2)

Arguments

img	Input image. Can be an antsImage of 2, 3 or 4 dimensions. If img is NULL, a file chooser dialog will appear.
lowThresh	An inclusive lower threshold for voxels to be included in the mask.
highThresh	An inclusive upper threshold for voxels to be included in the mask.
cleanup	If >0, morphological operations will be applied to clean up the mask by eroding away small or weakly-connected areas, and closing holes.

Details

If cleanup is >0, the following steps are applied

1. Erosion with radius 2 voxels

2. Retain largest component

3. Dilation with radius 1 voxel

4. Morphological closing

These functions are available in iMath, see the operations “ME”, “GetLargestComponent”, “MD”, “FillHoles”.

Value

Object of type antsImage containing the mask image. The voxel intensities will be binarized, 1 for voxels in the mask and 0 outside.

Author(s)

Shrinidhi KL, Cook PA, Avants BB

Examples

img <- ri(1)
mask <- getMask(img)
testthat::expect_error(getMask(img, lowThresh = "hey"))
pixeltype(img) <- "unsigned int"
mask2 <- getMask(img)

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.