threeBrain (version 1.0.1)

generate_smooth_envelope: Generate smooth envelope around surface

Description

Alternative to 'Matlab' version of 'pial-outer-smoothed', use this function along with fill_surface.

Usage

generate_smooth_envelope(
  surface_path,
  save_as = NULL,
  inflate = 3,
  verbose = TRUE,
  save_format = c("auto", "bin", "asc", "vtk", "ply", "off", "obj", "gii", "mz3", "byu")
)

Value

A 3-dimensional mesh that contains vertices and face indices, the result is also saved to save_as is specified.

Arguments

surface_path

path to '*h.pial' surface in the 'FreeSurfer' folder, or a 3-dimensional mesh, see read.fs.surface

save_as

save final envelope to path, or NULL for dry-run

inflate

number of 'voxels' to inflate before fitting envelope; must be a non-negative integer

verbose

whether to verbose the progress; default is true

save_format

format of saved file when save_as is not NULL; see format argument in function write.fs.surface

Examples

if(interactive() &&
   file.exists(file.path(default_template_directory(), "N27"))) {

library(threeBrain)

fs_path <- file.path(default_template_directory(), "N27")

# lh.pial-outer-smoothed
lh_pial <- file.path(fs_path, "surf", "lh.pial")
save_as <- file.path(fs_path, "surf", "lh.pial-outer-smoothed")
generate_smooth_envelope(lh_pial, save_as)

# rh.pial-outer-smoothed
rh_pial <- file.path(fs_path, "surf", "rh.pial")
save_as <- file.path(fs_path, "surf", "rh.pial-outer-smoothed")
generate_smooth_envelope(rh_pial, save_as)

brain <- threeBrain(
  path = fs_path, subject_code = "N27",
  surface_types = 'pial-outer-smoothed'
)
brain$plot(controllers = list(
  "Surface Type" = 'pial-outer-smoothed'
))

}