Volumetric segmentation to 3d-atlas — make_volumetric_2

Function to create a ggseg3d-atlas from a volumetric parcellation. Currently only tested using .mgz extension images. Will call command-line tools to complete the process.

make_volumetric_2_3datlas(
  template,
  color_lut,
  subject = "fsaverage5",
  subjects_dir = freesurfer::fs_subj_dir(),
  steps = 1:5,
  output_dir = tempdir(),
  verbose = TRUE,
  ncores = parallel::detectCores() - 2,
  cleanup = TRUE
)

Arguments

template	template `volume.mgz` file path
color_lut	Freesurfer colour look-up-table. Either as a path or a data.frame that `is_ctab`
subject	Freesurfer subject, must exist in whatever subject directory specified or set in the environment with $SUBJECTS_DIR
subjects_dir	Freesurfer subject directory
steps	if cleanup is disabled, all files are saved, and steps can be re-run individually
output_dir	output directory path
verbose	logical indicating to be verbose or not
ncores	number of cores for parallel processing (default numcores-2)
cleanup	logical to toggle removal of all intermediary files

Value

returns a ggseg3d-atlas ready object. Might need manual cleaning to become a good atlas.

Details

the function is aggressive in the number of cores used to minimize time taken to create the atlas. Set the ncores argument for less aggressive approach.

Examples

if (FALSE) {

fs_subject_dir <- freesurfer::fs_dir()
aseg_temp <- file.path(fs_subject_dir, "fsaverage5/mri/aseg.mgz")
colorlut <- file.path(fs_subject_dir, "ASegStatsLUT.txt")

make_volumetric_2_3datlas(aseg_temp, colorlut)
}