make_volumetric_ggseg: Make ggseg atlas from volumetric template

In LCBC-UiO/ggsegExtra: Extra Utilities for the 'ggseg' and 'ggseg3d' Plotting Tools

Make ggseg atlas from volumetric template

Description

If making an atlas from a non-cortical atlas, volumetric atlases are the best options. Instead of snapshotting images of inflated brain, will snapshot brain slices given x, y, z coordinates for the slices trhoush the slices argument.

Usage

make_volumetric_ggseg(
  label_file,
  subject = "fsaverage5",
  subjects_dir = fs_subj_dir(),
  output_dir = tempdir(),
  color_lut = NULL,
  steps = 1:8,
  skip_existing = TRUE,
  slices = data.frame(x = c(130, 122, 122), y = c(130, 235, 112), z = c(130, 100, 106),
    view = c("axial", "sagittal", "coronal"), stringsAsFactors = FALSE),
  vertex_size_limits = NULL,
  dilate = NULL,
  tolerance = 0,
  ncores = 2,
  smoothness = 5,
  verbose = TRUE,
  cleanup = FALSE
)

Arguments

label_file	a volumetric image containing the labels
subject	Freesurfer subject, must exist in whatever subject directory specified or set in the environment with $SUBJECTS_DIR
subjects_dir	Freesurfer subject directory
output_dir	output directory path
color_lut	a file containing color information for the labels
steps	numeric vector of steps to run
skip_existing	logical. If slice snapshots already exist, should these be skipped.
slices	a data.frame with columns x, y, z, and view specifying coordinates and view of slice snapshots.
vertex_size_limits	numeric vector of two, setting the minimum and maximum vector size of polygons. Defaults to NULL, which sets no limits.
dilate	numeric. Dilation factor for polygons. Default NULL applies no dilation.
tolerance	tolerance during vertex reduction st_simplify
ncores	number of cores for parallel processing (default numcores-2)
smoothness	smoothing factor, argument to smooth
verbose	logical indicating to be verbose or not
cleanup	logical to toggle removal of all intermediary files

Value

brain-atlas class

Examples

## Not run: 

   label_file <- file.path(fs_subj_dir(), subject, "mri/aseg.mgz")
   slices = data.frame(x=130, y=130, z=130, view="axial", stringsAsFactors = FALSE)
   
   aseg2 <- make_volumetric_ggseg(
      label_file =  label_file,
      slices = slices
   )

   # Have a look at the atlas
   plot(aseg2)

## End(Not run)

LCBC-UiO/ggsegExtra documentation built on May 9, 2022, 1:07 a.m.