Read a data annotation file in FreeSurfer format. Such a file assigns a label and a color to each vertex of a brain surface. The assignment of labels to vertices is based on at atlas or brain parcellation file. Typically the atlas is available for some standard template subject, and the labels are assigned to another subject by registering it to the template. For a subject (MRI image pre-processed with FreeSurfer) named 'bert', an example file would be 'bert/label/lh.aparc.annot', which contains the annotation based on the Desikan-Killiany Atlas for the left hemisphere of bert.
read.fs.annot(filepath, empty_label_name = "unknown", metadata = list())| filepath | string. Full path to the input annotation file. Note: gzipped files are supported and gz format is assumed if the filepath ends with ".gz". |
|---|---|
| empty_label_name | string. Ignored, deprecated. |
| metadata | named list of arbitrary metadata to store in the instance. |
named list, entries are: "vertices" vector of n vertex indices, starting with 0. "label_codes": vector of n integers, each entry is a color code, i.e., a value from the 5th column in the table structure included in the "colortable" entry (see below). "label_names": the n brain structure names for the vertices, already retrieved from the colortable using the code. "hex_colors_rgb": Vector of hex color for each vertex. The "colortable" is another named list with 3 entries: "num_entries": int, number of brain structures. "struct_names": vector of strings, the brain structure names. "table": numeric matrix with num_entries rows and 5 colums. The 5 columns are: 1 = color red channel, 2=color blue channel, 3=color green channel, 4=color alpha channel, 5=unique color code. "colortable_df": The same information as a dataframe. Contains the extra columns "hex_color_string_rgb" and "hex_color_string_rgba" that hold the color as an RGB(A) hex string, like "#rrggbbaa".
Other atlas functions:
colortable.from.annot(),
read.fs.colortable(),
write.fs.annot.gii(),
write.fs.annot(),
write.fs.colortable()
annot_file = system.file("extdata", "lh.aparc.annot.gz",
package = "freesurferformats",
mustWork = TRUE);
annot = read.fs.annot(annot_file);
print(annot);
#> Brain surface annotation assigning 149244 vertices to 36 brain regions.
#> - region #1 'unknown': size 0 vertices
#> - region #2 'bankssts': size 1722 vertices
#> - region #3 'caudalanteriorcingulate': size 1067 vertices
#> - region #4 'caudalmiddlefrontal': size 4179 vertices
#> - region #5 'corpuscallosum': size 0 vertices
#> - region #6 'cuneus': size 2183 vertices
#> - region #7 'entorhinal': size 718 vertices
#> - region #8 'fusiform': size 4773 vertices
#> - region #9 'inferiorparietal': size 7930 vertices
#> - region #10 'inferiortemporal': size 5138 vertices
#> - region #11 'isthmuscingulate': size 1479 vertices
#> - region #12 'lateraloccipital': size 8827 vertices
#> - region #13 'lateralorbitofrontal': size 4426 vertices
#> - region #14 'lingual': size 3693 vertices
#> - region #15 'medialorbitofrontal': size 3484 vertices
#> - region #16 'middletemporal': size 5546 vertices
#> - region #17 'parahippocampal': size 1254 vertices
#> - region #18 'paracentral': size 2293 vertices
#> - region #19 'parsopercularis': size 2444 vertices
#> - region #20 'parsorbitalis': size 1145 vertices
#> - region #21 'parstriangularis': size 2089 vertices
#> - region #22 'pericalcarine': size 1830 vertices
#> - region #23 'postcentral': size 7514 vertices
#> - region #24 'posteriorcingulate': size 1766 vertices
#> - region #25 'precentral': size 8410 vertices
#> - region #26 'precuneus': size 5987 vertices
#> - region #27 'rostralanteriorcingulate': size 1204 vertices
#> - region #28 'rostralmiddlefrontal': size 9447 vertices
#> - region #29 'superiorfrontal': size 12569 vertices
#> - region #30 'superiorparietal': size 8110 vertices
#> - region #31 'superiortemporal': size 6987 vertices
#> - region #32 'supramarginal': size 6656 vertices
#> - region #33 'frontalpole': size 416 vertices
#> - region #34 'temporalpole': size 637 vertices
#> - region #35 'transversetemporal': size 828 vertices
#> - region #36 'insula': size 4099 vertices