Write annotation to binary file.

Write an annotation to a FreeSurfer binary format annotation file in the new format (v2). An annotation (or brain parcellation) assigns each vertex to a label (or region). One of the regions is often called 'unknown' or similar and all vertices which are not relevant for the parcellation are assigned this label.

write.fs.annot(
  filepath,
  num_vertices = NULL,
  colortable = NULL,
  labels_as_colorcodes = NULL,
  labels_as_indices_into_colortable = NULL,
  fs.annot = NULL
)

Arguments

filepath	string, path to the output file
num_vertices	integer, the number of vertices of the surface. Must be given unless parameter `fs.annot` is not NULL.
colortable	dataframe that contains one region per row. Required columns are: 'struct_name': character string, the region name. 'r': integer in range 0-255, the RGB color value for the red channel. 'g': same for the green channel. 'b': same for the blue channel. 'a': the alpha (transparency) channel value. Optional columns are: 'code': the color code. Will be computed if not set. Note that you can pass the dataframe returned by read.fs.annot as 'colortable_df'. Only required if `labels_as_indices_into_colortable` is used.
labels_as_colorcodes	vector of *n* integers. The first way to specify the labels. Each integer is a colorcode, that has been computed from the RGBA color values of the regions in the colortable as r + g*2^8 + b*2^16 + a*2^24. If you do not already have these color codes, it is way easier to set this to NULL and define the labels as indices into the colortable, see parameter `labels_as_indices_into_colortable`.
labels_as_indices_into_colortable	vector of *n* integers, the second way to specify the labels. Each integer is an index into the rows of the colortable. Indices start with 1. This parameter and `labels_as_colorcodes` are mutually exclusive, but required.
fs.annot	instance of class `fs.annot`. If passed, this takes precedence over all other parameters and they should all be NULL (with the exception of `filepath`).

See also

Other atlas functions: colortable.from.annot(), read.fs.annot(), read.fs.colortable(), write.fs.annot.gii(), write.fs.colortable()

Examples

# \donttest{
   # Load annotation
   annot_file = system.file("extdata", "lh.aparc.annot.gz",
                               package = "freesurferformats",
                               mustWork = TRUE);
   annot = read.fs.annot(annot_file);

   # New method: write the annotation instance:
   write.fs.annot(tempfile(fileext=".annot"), fs.annot=annot);

   # Old method: write it from its parts:
   write.fs.annot(tempfile(fileext=".annot"), length(annot$vertices),
    annot$colortable_df, labels_as_colorcodes=annot$label_codes);
# }