fslr (version 1.0)

fslfill: Fill image holes

Description

This function calls fslmaths -fillh to fill in image holes and either saves the image or returns an object of class nifti

Usage

fslfill(file, outfile = NULL, bin = TRUE, retimg = FALSE,
  reorient = FALSE, intern = TRUE, ...)

Arguments

file

(character) filename of image to be filled

outfile

(character) name of resultant filled file

bin

(logical) binarize the image before filling

retimg

(logical) return image of class nifti

reorient

(logical) If retimg, should file be reoriented when read in? Passed to readNIfTI.

intern

(logical) pass to system

...

additional arguments passed to readNIfTI.

Value

• character or logical depending on intern

Examples

if (have.fsl()){
system.time({
x = array(rnorm(1e6), dim = c(100, 100, 100))
img = nifti(x, dim= c(100, 100, 100),
datatype = convert.datatype()$FLOAT32, cal.min = min(x),
cal.max = max(x), pixdim = rep(1, 4))
mask = img > .5
eroded = fslerode(mask, kopts = "-kernel boxv 5", retimg=TRUE)
filled = fslfill(eroded, retimg= TRUE)
})
}