fsbrain (version 0.5.5)

vis.region.values.on.subject: Visualize arbitrary data, one value per atlas region, on the surface of any subject (including template subjects).

Description

This function can be used for rendering a single value (color) for all vertices of an atlas region. The typical usecase is the visualization of results of atlas-based analyses, e.g., p-value, means or other aggregated values over all vertices of a region.

Usage

vis.region.values.on.subject(
  subjects_dir,
  subject_id,
  atlas,
  lh_region_value_list,
  rh_region_value_list,
  surface = "white",
  views = c("t4"),
  rgloptions = rglo(),
  rglactions = list(),
  value_for_unlisted_regions = NA,
  draw_colorbar = FALSE,
  makecmap_options = mkco.heat(),
  bg = NULL,
  silent = FALSE,
  style = "default",
  border = NULL
)

Value

list of coloredmeshes. The coloredmeshes used for the visualization.

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.

subject_id

string. The subject identifier.

atlas

string. The brain atlas to use. E.g., 'aparc' or 'aparc.a2009s'.

lh_region_value_list

named list. A list for the left hemisphere in which the names are atlas regions, and the values are the value to write to all vertices of that region. You can pass an unnamed list, but then the its length must exactly match the number of atlas regions. The order of values must also match the order of regions in the annotation, of course. The resulting mapping will be printed so you can check it (unless 'silent' is set).

rh_region_value_list

named list. A list for the right hemisphere in which the names are atlas regions, and the values are the value to write to all vertices of that region.

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.

value_for_unlisted_regions

numerical scalar or `NA`, the value to assign to regions which do not occur in the region_value_lists. Defaults to `NA`.

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'.

bg

a background definition. Can be a surface color layer or a character string like 'curv_light' to select a pre-defined layer, see collayer.bg for valid strings.

silent

logical, whether to suppress mapping info in case of unnamed region value lists (see 'lh_region_value_list' description).

style

character string, a rendering style, e.g., 'default', 'shiny' or 'semitransparent'.

border

logical, whether to add a black border around the regions. Alternatively, the parameter can be given as a named list with entries 'color' and 'expand_inwards', where the latter defines the borders thickness. E.g., border = list('color'='#FF0000', 'expand_inwards'=2L). Border computation is slow, sorry.

See Also

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.labeldata.on.subject(), vis.mask.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()

Other region-based visualization functions: vis.subject.annot()

Examples

if (FALSE) {
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   atlas = 'aparc';   # Desikan atlas
   # For the left hemisphere, we just assign a subset of the
   # atlas regions. The others will get the default value.
   lh_region_value_list = list("bankssts"=0.9, "precuneus"=0.7, "postcentral"=0.8, "lingual"=0.6);
   # For the right hemisphere, we retrieve the full list of regions for
   # the atlas, and assign random values to all of them.
   atlas_region_names = get.atlas.region.names(atlas, template_subjects_dir = subjects_dir,
    template_subject='subject1');
   rh_region_value_list = rnorm(length(atlas_region_names), 3.0, 1.0);
   names(rh_region_value_list) = atlas_region_names;
   vis.region.values.on.subject(subjects_dir, 'subject1', atlas,
    lh_region_value_list, rh_region_value_list);
}