mri_watershed {freesurfer}

Use Freesurfers MRI Watershed Algorithm

Description

This function calls mri_watershed to extract a brain from an image, usually for skull stripping.

Usage

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

Arguments

file

(character) input filename

outfile

(character) output filename

retimg

(logical) return image of class nifti

opts

(character) additional options to mri_watershed

...

additional arguments passed to fs_cmd.

Value

Character or nifti depending on retimg

Examples

## Not run: 
if (have_fs()){
    mri_watershed("/path/to/T1.nii.gz")
} 

## End(Not run)