Convert volume to label

Converts values in a volume or surface overlay to a label. The program searches the input for values equal to labelid. The xyz values for each point are then computed based on the tkregister voxel-to-RAS matrix (volume) or from the xyz of the specified surface. The xyz values are then stored in labelfile in the label file format. The statistic value is set to 0. While this program can be used with any mri volume, it was designed to convert parcellation volumes, which happen to be stored in mri format. Calls FreeSurfer's mri_vol2label.

mri_vol2label(
  input_file,
  label_id,
  hemisphere,
  output_dir,
  surface = NULL,
  subject = "fsaverage5",
  subjects_dir = fs_subj_dir(),
  opts = NULL,
  verbose = TRUE
)

Arguments

input_file	input volume
label_id	label to run
hemisphere	hemisphere, either "rh" or "lh"
output_dir	output directory path
surface	output surface
subject	Freesurfer subject, must exist in whatever subject directory specified or set in the environment with $SUBJECTS_DIR
subjects_dir	Freesurfer subject directory
opts	other arguments to freesurfer command
verbose	logical indicating to be verbose or not

Value

returns nothing. Writes a label file.

Examples

if(freesurfer::have_fs()){
# for freesurfer help see:
freesurfer::fs_help("mri_vol2label")

out_dir <- tempdir()
vol <- file.path(freesurfer::fs_subj_dir(),
                 "fsaverage5/mri/aseg.mgz")

mri_vol2label(vol, 
     label_id = 2, 
     hemisphere = "rh", 
     output_dir = out_dir)
 
 # delete output dir when not needed
 unlink(out_dir)
}