Generate surface file from 'nii' or 'mgz' volume files

Generate surface file from 'nii' or 'mgz' volume files

Usage

volume_to_surf(
  volume,
  save_to = NA,
  lambda = 0.2,
  degree = 2,
  threshold_lb = 0.5,
  threshold_ub = NA,
  format = "auto"
)

Arguments

volume

path to the volume file, or object from read_volume.

save_to

where to save the surface file; default is NA (no save).

lambda

'Laplacian' smooth, the higher the smoother

degree

'Laplacian' degree; default is 2

threshold_lb

lower threshold of the volume (to create mask); default is 0.5

threshold_ub

upper threshold of the volume; default is NA (no upper bound)

format

The format of the file if save_to is a valid path, choices include

'auto'

Default, supports 'FreeSurfer' binary format and 'ASCII' text format, based on file name suffix

'bin'

'FreeSurfer' binary format

'asc'

'ASCII' text format

'ply'

'Stanford' 'PLY' format

'off'

Object file format

'obj'

'Wavefront' object format

'gii'

'GIfTI' format. Please avoid using 'gii.gz' as the file suffix

'mz3'

'Surf-Ice' format

'byu'

'BYU' mesh format

'vtk'

Legacy 'VTK' format

'gii', otherwise 'FreeSurfer' format. Please do not use 'gii.gz' suffix.

Value

Triangle 'rgl' mesh (vertex positions in native 'RAS'). If save_to is a valid path, then the mesh will be saved to this location.

See also

read_volume, vcg_isosurface, vcg_smooth_implicit

Examples

library(threeBrain)
N27_path <- file.path(default_template_directory(), "N27")
if(dir.exists(N27_path)) {
  aseg <- file.path(N27_path, "mri", "aparc+aseg.mgz")

  # generate surface for left-hemisphere insula
  mesh <- volume_to_surf(aseg, threshold_lb = 1034,
                         threshold_ub = 1036)

  if(interactive()) {
    ravetools::rgl_view({
      ravetools::rgl_call("shade3d", mesh, color = "yellow")
    })
  }
}