View source: R/write_fs_annot.R
write.fs.annot | R Documentation |
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
)
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 |
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 |
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'). |
Other atlas functions:
colortable.from.annot()
,
read.fs.annot()
,
read.fs.colortable()
,
write.fs.annot.gii()
,
write.fs.colortable()
## Not run:
# 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);
## End(Not run)
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