label.to.annot {fsbrain}

Merge several labels into an annotation

Description

Merge several labels and a colortable into an annotation.

Usage

label.to.annot(
  label_vertices_by_region,
  num_vertices_in_surface,
  colortable_df = NULL,
  index_of_unknown_region = 1L
)

Arguments

label_vertices_by_region

named list of integer vectors, the keys are strings which define region names, and the values are integer vectors: the vertex indices of the region.

num_vertices_in_surface

integer, total number of vertices in the surface mesh

colortable_df

NULL or dataframe, a colortable. It must contain the columns 'struct_name', 'r', 'g', 'b', and 'a'. All other columns will be derived if missing. The entries in 'struct_name' must match keys from the 'label_vertices_by_region' parameter. There must be one more row in here than there are labels. This row identifies the 'unknown' region (see also parameter 'index_of_unknown_region'). If NULL, a colortable will be auto-generated.

index_of_unknown_region

positive integer, the index of the row in 'colortable_df' that defines the 'unknown' or 'background' region to which all vertices will be assigned which are *not* part of any of the given labels.

Value

an annotation, see read.fs.annot for details.

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(), regions.to.ignore(), spread.values.over.annot(), spread.values.over.hemi(), spread.values.over.subject(), subject.annot(), subject.atlas.agg(), subject.label.from.annot(), subject.lobes()

Examples

  # Create two labels. Real-word labels would have more vertices, of course.
  label1 = c(46666, 467777);
  label2 = c(99888, 99889);
  label_vertices = list("region1"=label1, "region2"=label2);
  colortable_df = data.frame("struct_index"=seq(0, 2),
   "struct_name"=c("unknown", "region1", "region2"),
   "r"=c(255L, 255L, 0L), "g"=c(255L, 0L, 255L), "b"=c(255L, 0L, 0L), "a"=c(0L, 0L, 0L));
  annot = label.to.annot(label_vertices, 100000, colortable_df);