fsbrain (version 0.0.2)

vis.mask.on.subject: Visualize a vertex mask on the surface of a subject.

Description

A mask is a logical vector that contains one value per vertex. You can create it manually, or use functions like [fsbrain::mask.from.labeldata.for.hemi] to create and modify it. Check the example for this function.

Usage

vis.mask.on.subject(subjects_dir, vis_subject_id, mask_lh, mask_rh,
  surface = "white", colormap = squash::rainbow2, views = c("t4"),
  rgloptions = list(), rglactions = list(), draw_colorbar = FALSE)

Arguments

subjects_dir,

string. The FreeSurfer SUBJECTS_DIR, containing the subdir of vis_subject_id, the subject that you want to use for visualization.

vis_subject_id,

string. The subject identifier from which to obtain the surface for data visualization. Example: 'fsaverage'.

mask_lh,

logical vector or NULL, the mask to visualize on the left hemisphere surface. Must have the same length as the lh surface of the vis_subject_id has vertices. If NULL, this surface will not be rendered. Only one of mask_lh or mask_rh is allowed to be NULL.

mask_rh,

logical vector or NULL, the mask to visualize on the right hemisphere surface. Must have the same length as the rh surface of the vis_subject_id has vertices. If NULL, this surface will not be rendered. Only one of mask_lh or mask_rh is allowed to be NULL.

surface,

string. The display surface. E.g., "white", "pial", or "inflated". Defaults to "white".

colormap,

a colormap. See the squash package for some colormaps. Defaults to [squash::jet].

views,

list of strings. Valid entries include: 'si': single interactive view. 't4': tiled view showing the brain from 4 angles. 't9': tiled view showing the brain from 9 angles.

rgloptions

option list passed to [rgl::par3d()]. Example: rgloptions = list("windowRect"=c(50,50,1000,1000));

rglactions,

named list. A list in which the names are from a set of pre-defined actions. The values can be used to specify parameters for the action.

draw_colorbar

logical, whether to draw a colorbar. WARNING: The colorbar is drawn to a subplot, and this only works if there is enough space for it. You will have to increase the plot size using the 'rlgoptions' parameter for the colorbar to show up. Defaults to FALSE.

Value

list of coloredmeshes. The coloredmeshes used for the visualization.

See Also

Other mask functions: coloredmesh.from.mask, mask.from.labeldata.for.hemi

Examples

# NOT RUN {
   fsbrain::download_optional_data();

  # Define the data to use:
  subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
  subject_id = 'subject1';
  surface = 'white';
  hemi = 'both';
  atlas = 'aparc';
  region = 'bankssts';

  # Create a mask from a region of an annotation:
  lh_annot = subject.annot(subjects_dir, subject_id, 'lh', atlas);
  rh_annot = subject.annot(subjects_dir, subject_id, 'rh', atlas);
  lh_label = label.from.annotdata(lh_annot, region);
  rh_label = label.from.annotdata(rh_annot, region);
  lh_mask = mask.from.labeldata.for.hemi(lh_label, length(lh_annot$vertices));
  rh_mask = mask.from.labeldata.for.hemi(rh_label, length(rh_annot$vertices));

  # Edit the mask: add the vertices from another region to it:
  region2 = 'medialorbitofrontal';
  lh_label2 = label.from.annotdata(lh_annot, region2);
  rh_label2 = label.from.annotdata(rh_annot, region2);
  lh_mask2 = mask.from.labeldata.for.hemi(lh_label2, length(lh_annot$vertices),
   existing_mask = lh_mask);
  rh_mask2 = mask.from.labeldata.for.hemi(rh_label2, length(rh_annot$vertices),
   existing_mask = rh_mask);
  # Visualize the mask:
  vis.mask.on.subject(subjects_dir, subject_id, lh_mask2, rh_mask2);
# }
# NOT RUN {
# }