vis.subject.morph.native: Visualize native space morphometry data for a subject.

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

Visualize native space morphometry data for a subject.

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.

Usage

vis.subject.morph.native(
  subjects_dir,
  subject_id,
  measure,
  hemi = "both",
  surface = "white",
  views = c("t4"),
  rgloptions = rglo(),
  rglactions = list(),
  draw_colorbar = FALSE,
  cortex_only = FALSE,
  style = "default",
  makecmap_options = mkco.seq(),
  bg = NULL
)

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.
measure	string. The morphometry data to use. E.g., 'area' or 'thickness'. Pass NULL to render just the surface in white, without any data.
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.
cortex_only	logical, whether to mask the medial wall, i.e., whether the morphometry data for all vertices which are *not* part of the cortex (as defined by the label file 'label/?h.cortex.label') should be replaced with NA values. In other words, setting this to TRUE will ignore the values of the medial wall between the two hemispheres. If set to true, the mentioned label file needs to exist for the subject. Defaults to FALSE.
style	character string, a rendering style, e.g., 'default', 'shiny' or 'semitransparent'.
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.

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.fsaverage(), 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.standard(), vis.subject.pre(), vis.symmetric.data.on.subject(), vislayout.from.coloredmeshes()

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

Examples

## Not run: 
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   vis.subject.morph.native(subjects_dir, 'subject1', 'thickness', 'lh', views=c("t9"));

## End(Not run)

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