Use Freesurfers MRI Mask — mri

This function calls mri_mask to mask an image

mri_mask(file, mask, outfile = NULL, retimg = TRUE, opts = "", ...)

Arguments

file	(character) input filename
mask	(character) mask filename
outfile	(character) output filename
retimg	(logical) return image of class nifti
opts	(character) additional options to `mri_mask`
...	additional arguments passed to `fs_cmd`.

Character or nifti depending on retimg

if (have_fs()) {
   img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5)))  
   mask = img > 1
   res = mri_mask(img, mask)
}