coloredmesh.from.morph.standard: Create a coloredmesh from standard space morphometry data.

Description Usage Arguments Value See Also

View source: R/coloredmesh.R

Description

Create a coloredmesh from standard space morphometry data.

Usage

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coloredmesh.from.morph.standard(
  subjects_dir,
  subject_id,
  measure,
  hemi,
  fwhm,
  surface = "white",
  template_subject = "fsaverage",
  template_subjects_dir = NULL,
  colormap = NULL,
  clip = NULL,
  cortex_only = FALSE,
  makecmap_options = mkco.seq()
)

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 the surface in white, without any data. One can also pass the pre-loaded morphometry data as a numerical vector, the length of which must match the number of surface vertices.

hemi

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

fwhm

string, smoothing setting. The smoothing part of the filename, typically something like '0', '5', '10', ..., or '25'.

surface

character string or 'fs.surface' instance. The display surface. E.g., "white", "pial", or "inflated". Defaults to "white".

template_subject

The template subject used. This will be used as part of the filename, and its surfaces are loaded for data visualization. Defaults to 'fsaverage'.

template_subjects_dir

The template subjects dir. If ‘NULL', the value of the parameter ’subjects_dir' is used. Defaults to NULL. If you have FreeSurfer installed and configured, and are using the standard fsaverage subject, try passing the result of calling 'file.path(Sys.getenv('FREESURFER_HOME'), 'subjects')'.

colormap

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

clip

numeric vector of length 2 or NULL. If given, the 2 values are interpreted as lower and upper percentiles, and the morph data is clipped at the given lower and upper percentile (see clip.data). Defaults to NULL (no data clipping).

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.

makecmap_options

named list of parameters to pass to makecmap. Must not include the unnamed first parameter, which is derived from 'measure'.

Value

coloredmesh. A named list with entries: "mesh" the tmesh3d mesh object. "col": the mesh colors. "render", logical, whether to render the mesh. "hemi": the hemisphere, one of 'lh' or 'rh'.

See Also

Other coloredmesh functions: coloredmesh.from.annot(), coloredmesh.from.label(), coloredmesh.from.mask(), coloredmesh.from.morph.native(), coloredmesh.from.morphdata(), coloredmeshes.from.color()


fsbrain documentation built on May 12, 2021, 5:06 p.m.