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3D Surface plotter

plot_surf3d.Rd

Plots 3D cortical surfaces

Usage

plot_surf3d(
  surf_data,
  surf_color = "grey",
  cmap,
  limits,
  atlas = 1,
  hemi = "b",
  medial_gap = 0,
  orientation_labels = TRUE,
  plot_grid = TRUE,
  transparent_bg = FALSE,
  smooth_mesh = 0,
  VWR_check = TRUE
)

Arguments

surf_data

A numeric vector (length of V), where V is the number of vertices. It can be the output from SURFvextract(), CAT12vextract(), FSLRvextract(), HIPvextract(), ASEGvextract().

surf_color

color of the cortical surface for NA values. Set to 'grey' by default. A RGBA string can also be given, with A as the opacity (0 to 1), e.g. for transparent grey: surf_color="rgba(100,100,100,0.5)".

cmap

A string vector containing 2 to 4 color names/codes specifying the colors to be used for the color scale; or a single string object with the name of a color map listed in RColorBrewer::display.brewer.all(). If none are specified, appropriate colors will be automatically selected according to range(surf_data)

limits

A combined pair of numeric vector composed of the lower and upper color scale limits of the plot. When left unspecified, the symmetrical limits c(-max(abs(surf_dat),max(abs(surf_dat))) will be used.

atlas

atlas used for identifying region labels. 1=Desikan, 2=Destrieux-148, 3=Glasser-360, 4=Schaefer-100, 5=Schaefer-200, 6=Schaefer-400. Set to 1 by default. This argument is ignored for HippUnfold hippocampal surfaces and SubCortexMesh subcortical surface.

hemi

A string specifying the hemisphere to plot. Possible values are l (left), r (right) or b (both).

medial_gap

A numeric value specifying the amount of gap (in MNI coordinate units) to separate the left and right hemispheres. Set to 0 (no gap between hemispheres) by default. In order to view the medial surfaces clearly, it is recommended that this value is set to 20. This argument is ignored if hemi!='b'

orientation_labels

A boolean object specifying if orientation labels are to be displayed. Set to TRUE by default

plot_grid

A boolean object specifying whether to plot the orientation grid or not (default is TRUE).

transparent_bg

A boolean object specifying whether to get a transparent background upon saving the image (default is FALSE, white background).

smooth_mesh

A numeric object stating the number of iterations of (Laplacian) smoothing to make the surface appear smoother. Not applicable for HippUnfold hippocampal data. Default is 0.

VWR_check

A boolean object specifying whether to check and validate system requirements. Default is TRUE.

Value

a plot_ly object

Examples

surf_data = runif(20484);
plot_surf3d(surf_data = surf_data, VWR_check=FALSE)
#> Non-interactive sessions need requirement checks