vis.data.on.fsaverage {fsbrain}

Visualize arbitrary data on the fsaverage template subject, if available.

Description

Creates a surface mesh, applies a colormap transform the morphometry data values into colors, and renders the resulting colored mesh in an interactive window. If hemi is 'both', the data is rendered for the whole brain. This function tries to automatically retrieve the subjects dir of the fsaverage template subject by checking the environment variables SUBJECTS_DIR and FREESURFER_HOME for the subject. The subject is required for its surfaces, which are not shipped with this package for licensing reasons.

Usage

vis.data.on.fsaverage(
  subjects_dir = NULL,
  vis_subject_id = "fsaverage",
  morph_data_lh = NULL,
  morph_data_rh = NULL,
  surface = "white",
  views = c("t4"),
  rgloptions = rglo(),
  rglactions = list(),
  draw_colorbar = FALSE,
  makecmap_options = mkco.seq(),
  bg = NULL,
  morph_data_both = 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.

vis_subject_id

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

morph_data_lh

numeric vector or character string or NULL, the data to visualize on the left hemisphere surface. If a string, it is treated as a filename and data is loaded from it first. When it is a numerical vector, this is assumed to be the data already. The data must have the same length as the surface of the vis_subject_id has vertices. If NULL, this surface will not be rendered. Only one of morph_data_lh or morph_data_rh is allowed to be NULL.

morph_data_rh

numeric vector or character string or NULL, the data to visualize on the right hemisphere surface. If a string, it is treated as a filename and data is loaded from it first. When it is a numerical vector, this is assumed to be the data already. The data must have the same length as the surface of the vis_subject_id has vertices. If NULL, this surface will not be rendered. Only one of morph_data_lh or morph_data_rh is allowed to be NULL.

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'.

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.

morph_data_both

numeric vector or NULL, the data to visualize on both hemispheres. This must be a single vector with length equal to the sum of the vertex counts of the left and the right hemisphere. The data for the left hemisphere must come first. If this is given, 'morph_data_lh' and 'morph_data_rh' must be NULL.

style

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

Value

list of coloredmeshes. The coloredmeshes used for the visualization.

See Also

Other visualization functions: highlight.vertices.on.subject.spheres(), highlight.vertices.on.subject(), vis.color.on.subject(), vis.data.on.subject(), vis.labeldata.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()

Other morphometry visualization functions: vis.data.on.subject(), vis.subject.morph.native(), vis.subject.morph.standard(), vis.symmetric.data.on.subject()