vis.labeldata.on.subject: Visualize a label on the surface of a subject.

In dfsp-spirit/nitools: Managing and Visualizing Brain Surface Data

Visualize a label on the surface of a subject.

Description

Visualizes a label. Note that a label is just a set of vertices, and that you can use this function to visualize sets of vertices, e.g., to see where on the mesh a certain vertex lies. It may be helpful the visualize the vertex with its neighbors, because otherwise it may be too small to spot. Use the function [fsbrain::mesh.vertex.neighbors] to get them. It is advisable to set the view to the interactive 'si' mode and use the 'inflated' surface to identify single vertices.

Usage

vis.labeldata.on.subject(
  subjects_dir,
  vis_subject_id,
  lh_labeldata,
  rh_labeldata,
  surface = "white",
  views = c("t4"),
  rgloptions = rglo(),
  rglactions = list(),
  draw_colorbar = FALSE,
  makecmap_options = list(colFn = label.colFn.inv),
  style = "default",
  ...
)

Arguments

subjects_dir	string. The FreeSurfer SUBJECTS_DIR, i.e., a directory containing the data for all your subjects, each in a subdir named after the subject identifier.
vis_subject_id	string. The subject identifier from which to obtain the surface for data visualization. Example: 'fsaverage'.
lh_labeldata	integer vector of vertex indices for the left hemisphere
rh_labeldata	integer vector of vertex indices for the right hemisphere
surface	string. The display surface. E.g., "white", "pial", or "inflated". Defaults to "white".
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 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. The following example clips outliers in the data before plotting and writes a screenshot in PNG format: rglactions = list("snapshot_png"="~/fsbrain.png", "clip_data"=c(0.05, 0.95)). See rglactions.
draw_colorbar	logical or one of the character strings 'vertical' or 'horizontal', whether to draw a colorbar. Notice: the colorbar is drawn to a separate subplot, and this only works if there is enough space for it, i.e., the plot resolution must be high enough. You may have to increase the plot size for the colorbar to show up, see the vignette for instructions. Defaults to 'FALSE'. See coloredmesh.plot.colorbar.separate for an alternative.
makecmap_options	named list of parameters to pass to makecmap. Must not include the unnamed first parameter, which is derived from 'measure'. Should include at least a colormap function as name 'colFn'.
style	character string, a rendering style, e.g., 'default', 'shiny' or 'semitransparent'.
...	extra arguments to pass to coloredmesh.from.label.

Value

list of coloredmeshes. The coloredmeshes used for the visualization.

Note

Drawing a colorbar for label data makes limited sense, use a legend instead. The colorbar can give a rough overview of the relative number of label and non-label vertices though, so it is possible to request one.

See Also

Other label functions: apply.label.to.morphdata(), apply.labeldata.to.morphdata(), subject.lobes(), subject.mask(), vis.subject.label()

Other visualization functions: highlight.vertices.on.subject.spheres(), highlight.vertices.on.subject(), vis.color.on.subject(), vis.data.on.fsaverage(), vis.data.on.subject(), vis.mask.on.subject(), vis.region.values.on.subject(), vis.subject.annot(), vis.subject.label(), vis.subject.morph.native(), vis.subject.morph.standard(), vis.subject.pre(), vis.symmetric.data.on.subject(), vislayout.from.coloredmeshes()

Examples

## Not run: 
   fsbrain::download_optional_data();

  # Define the data to use:
  subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
  lh_labeldata = c(1000, 1001, 1002);   # only the vertices, will be tiny.
  subject_id = 'subject1';
  surface = 'white'; # Should use 'inflated', but we do not currently
                     # ship it for the example subject to reduce download size.

  # For the right hemi, extend them to neighborhood for better visibility:
  rh_labeldata = c(500, 5000);
  rh_surface = subject.surface(subjects_dir, subject_id, surface, 'rh');
  rh_labeldata_neighborhood = mesh.vertex.neighbors(rh_surface, rh_labeldata);
  vis.labeldata.on.subject(subjects_dir, subject_id, lh_labeldata,
   rh_labeldata_neighborhood$vertices, surface=surface, views=c('si'));

## End(Not run)

dfsp-spirit/nitools documentation built on Jan. 26, 2024, 8:24 p.m.