blobness3D {vesselr}

3D Volume Blobness

Description

This function returns a blobness map for a 3D array or NIfTI volume. This blobness measure is based on the volume ratio described by Pierpaoli and Basser (1996).

Usage

blobness3D(image, mask, radius = 5, color = "dark", parallel = FALSE,
  cores = 2)

Arguments

image

a 3D array or image of class nifti

mask

an array or nifti mask of voxels for which vesselness will be calculated, with more selective masking improving speed significantly. Note that mask should be in the same space as the image volume

radius

an integer specifying radius of the neighborhood (in voxels) for which the blobness should be calculated. Note that this value essentially serves as the scale of the blob objects

color

a string specifying whether blobs will appear darker ("dark") or brighter ("bright") than their surroundings

parallel

is a logical value that indicates whether the user's computer is Linux or Unix (i.e. macOS), and should run the code in parallel

cores

if parallel = TRUE, cores is an integer value that indicates how many cores the function should be run on

Value

A 3D volume of the volume ratio blobness scores.

References

C. Pierpaoli, P.J. Basser (1996). Toward a Quantitative Assessment of Diffusion Anisotropy. Magnetic Resonance in Medicine. 36, pp. 893-906.

Examples

## Not run: 
library(neurobase)
flair <- readnii('path/to/epi')
mask <- flair!=0
brightspots <- blobness3D(image = flair, mask = mask, radius = 5,
                      color = "bright", parallel = TRUE, cores = 4) 
## End(Not run)