spread.values.over.hemi: Spread the values in the region_value_list and return them...

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

Spread the values in the region_value_list and return them for one hemisphere.

Description

Given an atlas and a list that contains one value for each atlas region, create morphometry data in which all region vertices are assigned the value. Can be used to plot stuff like p-values or effect sizes onto brain regions.

Usage

spread.values.over.hemi(
  subjects_dir,
  subject_id,
  hemi,
  atlas,
  region_value_list,
  value_for_unlisted_regions = NA,
  silent = 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
hemi	string, one of 'lh' or 'rh'. The hemisphere name. Used to construct the names of the annotation and morphometry data files to be loaded.
atlas	string. The atlas name. E.g., "aparc", "aparc.2009s", or "aparc.DKTatlas". Used to construct the name of the annotation file to be loaded.
region_value_list	named list. A list in which the names are atlas regions, and the values are the value to write to all vertices of that region. You can pass an unnamed list or vector, but then the length must exactly match the number of regions in the atlas, and the order must match the annotation file of the subject and hemisphere. Use with care, and keep in mind that some subjects do not have all regions.
value_for_unlisted_regions	numeric scalar. The value to assign to vertices which are part of atlas regions that are not listed in region_value_list. Defaults to NaN.
silent	logical, whether to suppress mapping info in case of unnamed region value lists (see 'lh_region_value_list' description).

Value

numeric vector containing the data.

See Also

Other atlas functions: get.atlas.region.names(), group.agg.atlas.native(), group.agg.atlas.standard(), group.annot(), group.label.from.annot(), label.from.annotdata(), label.to.annot(), regions.to.ignore(), spread.values.over.annot(), spread.values.over.subject(), subject.annot(), subject.atlas.agg(), subject.label.from.annot(), subject.lobes()

Examples

## Not run: 
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   region_value_list = list("bankssts"=0.9, "precuneus"=0.7);
   morph_like_data =
   spread.values.over.hemi(subjects_dir, 'subject1', 'lh', 'aparc', region_value_list);

## End(Not run)

dfsp-spirit/fsbrain documentation built on Nov. 28, 2024, 10:29 a.m.