Generate surface file from 'nii'
or 'mgz'
volume files
Source: R/utils_generate_subcortical_surf.R
volume_to_surf.Rd
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 is2
- 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.
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")
})
}
}