mri_mask: Use Freesurfers MRI Mask

In freesurfer: Wrapper Functions for 'Freesurfer'

Use Freesurfers MRI Mask

Description

This function calls mri_mask to mask an image

Usage

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.

Value

Character or nifti depending on retimg

Examples

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

freesurfer documentation built on June 8, 2025, 10:17 a.m.