vis.subject.label: Visualize a binary label for a subject.

Description Usage Arguments Value Note See Also Examples

View source: R/vis.R

Description

Visualize a label for a subject. A label is just a logical vector with one entry for each vertex in the mesh. Each vertex may additionally be associated with a scalar value, but this function ignored that.

Usage

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vis.subject.label(
  subjects_dir,
  subject_id,
  label,
  hemi,
  surface = "white",
  views = c("t4"),
  rgloptions = rglo(),
  rglactions = list(),
  draw_colorbar = FALSE,
  makecmap_options = list(colFn = label.colFn.inv, col.na = "#FFFFFF00"),
  map_to_NA = 0L,
  bg = NULL,
  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.

subject_id

string. The subject identifier.

label

string. Name of the label file, without the hemi part (if any), but including the '.label' suffix. E.g., 'cortex.label' for '?h.cortex.label'.

hemi

string, one of 'lh', 'rh', or 'both'. The hemisphere name. Used to construct the names of the label data files to be loaded.

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'.

map_to_NA

the value or value range that should **not** be considered part of the label, and should thus be plotted as background color. Only used if 'bg' is not 'NULL'. If a single value, only excatly this value is used (typically 0). If two values, they are interpreted as a range, and a values between them are mapped to NA. If you prefer to map the data to NA yourself before using this function, pass 'NULL'.

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.

style

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

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 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.region.values.on.subject(), vis.subject.annot(), vis.subject.morph.native(), vis.subject.morph.standard(), vis.subject.pre(), vis.symmetric.data.on.subject(), vislayout.from.coloredmeshes()

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

Examples

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   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   subject_id = 'subject1';
   surface = 'white';
   hemi = 'both';
   label = 'cortex.label';
   vis.subject.label(subjects_dir, subject_id, label, hemi, views="si");

fsbrain documentation built on Sept. 16, 2021, 5:07 p.m.