Extract color lookup table (LUT) from annotation.

Extract a colortable lookup table (LUT) from an annotation. Such a LUT can also be read from files like FREESURFER_HOME/FreeSurferColorLUT.txt or saved as a file, check the 'See Also' section below.

Usage

colortable.from.annot(annot, compute_colorcode = FALSE)

Arguments

annot

An annotation, as returned by read.fs.annot. If you want to assign specific indices, you can add a column named 'struct_index' to the data.frame annot$colortable_df. If there is no such columns, the indices will be created automatically in the order of the regions, starting at zero.

compute_colorcode

logical, indicates whether the unique color codes should be computed and added to the returned data.frame as an extra integer column named 'code'. Defaults to FALSE.

Value

the colortable data.frame extracted from the annotation.

See also

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

Other colorLUT functions: read.fs.colortable(), write.fs.colortable()

Examples

annotfile <- system.file("extdata", "lh.aparc.annot.gz",
  package = "freesurferformats", mustWork = TRUE
)
annot <- read.fs.annot(annotfile)
colortable <- colortable.from.annot(annot)
head(colortable)
#>   struct_index             struct_name   r   g   b a
#> 1            0                 unknown  25   5  25 0
#> 2            1                bankssts  25 100  40 0
#> 3            2 caudalanteriorcingulate 125 100 160 0
#> 4            3     caudalmiddlefrontal 100  25   0 0
#> 5            4          corpuscallosum 120  70  50 0
#> 6            5                  cuneus 220  20 100 0