read.fs.annot.gii {freesurferformats}

Read an annotation or label in GIFTI format.

Description

Read an annotation or label in GIFTI format.

Usage

read.fs.annot.gii(
  filepath,
  element_index = 1L,
  labels_only = FALSE,
  rgb_column_names = c("Red", "Green", "Blue", "Alpha"),
  key_column_name = "Key",
  empty_label_name = "unknown"
)

Arguments

filepath

string. Full path to the input label file in GIFTI format.

element_index

positive integer, the index of the dataarray to return. Ignored unless the file contains several dataarrays.

labels_only

logical, whether to ignore the colortable and region names. The returned annotation will only contain the a vector that contains one integer label per vertex (as entry 'label_codes'), but no region names and colortable information.

rgb_column_names

vector of exactly 4 character strings, order is important. The column names for the red, green, blue and alpha channels in the lable table. If a column does not exist, pass NA. If you do not know the column names, just call the function, it will print them. See 'labels_only' if you do not care.

key_column_name

character string, the column name for the key column in the lable table. This is the column that holds the label value from the raw vector (see 'labels_only') that links a label value to a row in the label table. Without it, one cannot recostruct the region name and color of an entry. Passing NA has the same effect as setting 'labels_only' to TRUE.

empty_label_name

character string, a base name to use to rename regions with empty name in the label table. This should not occur, and you can ignore this parameter setting. A warning will be thrown if this ever triggers. Not to be confused with parameter default_label_name, see below.

See Also

Other gifti readers: read.fs.label.gii(), read.fs.morph.gii(), read.fs.surface.gii()