fsbrain (version 0.0.3)

vis.subject.morph.native: 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", colormap = squash::jet,
  views = c("t4"), rgloptions = list(), rglactions = list(),
  draw_colorbar = FALSE, cortex_only = FALSE)

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.'

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".

colormap

a colormap. See the squash package for some colormaps. Defaults to jet.

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.

draw_colorbar

logical, whether to draw a colorbar. WARNING: The colorbar is drawn to a subplot, and this only works if there is enough space for it. You will have to increase the plot size using the 'rlgoptions' parameter for the colorbar to show up. Defaults to FALSE. See [fsbrain::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.

Value

list of coloredmeshes. The coloredmeshes used for the visualization.

See Also

Other visualization functions: 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, vislayout.from.coloredmeshes

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

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');
# }
# NOT RUN {
# }