clusterinfo_from_thresholded_overlay: Create clusterinfo instance from thresholded per-vertex data...

In dfsp-spirit/brainloc: Find Region Names and Coordinates for a Point on the Human Brain

Description

Create clusterinfo instance from thresholded per-vertex data overlays.

Usage

clusterinfo_from_thresholded_overlay(
  lh_threshmap,
  rh_threshmap,
  value_thresholded = 0,
  template_subject = "fsaverage",
  subjects_dir = file.path(getOption("brainloc.fs_home", default =
    Sys.getenv("FREESURFER_HOME")), "subjects")
)

Arguments

lh_threshmap	double vector, the stats map. Typically a thresholded t-value map. Must have one value per vertex. The value assigned to vertices that have been removed by the thresholding can be set with parameter 'value_thresholded'. If a character string, the parameter will be interpreted as file path and loaded with freesurferformats::read.fs.morph.
rh_threshmap	like lh_threshmap, but for the right hemisphere.
value_thresholded	scalar double, the data value of thresholded vertices in the lh_threshmap and rh_threshmap.
template_subject	character string, the template subject name. Typically 'fsaverage' or 'fsaverage6'. Must be some MNI305 space subject.
subjects_dir	character string, file system path to a directory containing the recon-all data for the template_subject. Used to load surfaces and annotations to identify cluster coordinates and atlas regions.

Value

a clusterinfo instance.

Note

This can only work if there are no clusters which touch each other. I think this can never happen, but we should double-check.

See Also

clusterinfo If you do have a separate t-map and a cluster overlay map instead of only a thresholded t-map.

dfsp-spirit/brainloc documentation built on Jan. 28, 2022, 12:25 p.m.