Erode image using FSL — fsl

This function calls fslmaths -ero to erode an image with either the default FSL kernel or the kernel specified in kopts. The function either saves the image or returns an object of class nifti.

fsl_erode(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslerode(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  kopts = "",
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

...: additional arguments passed to readnii.
outfile: (character) resultant eroded image name
retimg: (logical) return image of class nifti
file: (character) image to be eroded
reorient: (logical) If retimg, should file be reoriented when read in? Passed to readnii.
intern: (logical) to be passed to system
kopts: (character) options for kernel
opts: (character) additional options to be passed to fslmaths
verbose: (logical) print out command before running

Value

Result from system command, depends if intern is TRUE or FALSE. If retimg is TRUE, then the image will be returned.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping

Examples

if (have.fsl()){
system.time({
dims = c(50, 50, 20)
x = array(rnorm(prod(dims)), dim = dims) 
img = nifti(x, dim= dims, 
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)
})
}    
#> fslmaths "/private/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T/RtmpKzob0N/file857530879a5c.nii.gz" -kernel boxv 5 -ero  "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpKzob0N/file857545b41004"
#>    user  system elapsed 
#>   0.326   0.003   0.330