MRI Deface — mri_deface • freesurfer

This calls Freesurfer's mri_deface

mri_deface(file, brain_template = NULL, face_template = NULL, ...)

Arguments

file	File to pass to `mri_deface`
brain_template	`gca` brain template file to pass to `mri_deface`
face_template	`gca` face template file to pass to `mri_deface`
...	Additional arguments to pass to `fs_cmd`

Value

Result of fs_cmd, which type depends on arguments to ...

Note

If brain_template orface_template is NULL, they will be downloaded.

Examples

# \donttest{
if (have_fs()){
   base_url = "https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface"
   url = file.path(base_url, "sample_T1_input.mgz")
   x = tempfile(fileext = ".mgz")
   out = try({
   utils::download.file(url, destfile = x)
   })
   if (!inherits(out, "try-error")) {
      noface = mri_deface(x)
   } else {
      url = paste0(
         "https://raw.githubusercontent.com/muschellij2/kirby21.t1/master/", 
         "inst/visit_1/113/113-01-T1.nii.gz")
      x = tempfile(fileext = ".nii.gz")
      out = try({
          utils::download.file(url, destfile = x)
      })
      noface = mri_deface(x)
   }
}
# }