freesurfer (version 1.8.1)

mri_synthstrip: Use Freesurfers MRI SynthStrip

Description

This function calls mri_mask to mask an image

Usage

mri_synthstrip(
  file,
  outfile = NULL,
  retimg = TRUE,
  maskfile = NULL,
  opts = "",
  ...
)
synthstrip(
  file,
  outfile = NULL,
  retimg = TRUE,
  maskfile = NULL,
  opts = "",
  ...
)

Value

Character or nifti depending on retimg

Arguments

file

(character) input filename

outfile

(character) output filename

retimg

(logical) return image of class nifti

maskfile

(character) path for mask output

opts

(character) additional options to mri_mask

...

additional arguments passed to fs_cmd.

Examples

if (have_fs() && requireNamespace("oro.nifti", quietly = TRUE)) {
   img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5)))  
   res = mri_synthstrip(img)
}