Script to read FreeSurfer Color LUT table in Python 3

read_freesurefer_lut.py

import numpy as np
import re

"""
The link to the table: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT
It is also available locally if FreeSurfer is installed: $FREESURFER_HOME/FreeSurferColorLUT.txt

Read and store FreeSufer LUT color table
The result is two variables:

rgb - numpy array where 0th dimention is the region code (first column) and 3 other 
dimensions are for RBG values. Final fimension: (number of regions x 3)

label_names - dictinory where key = region code, and value = label name
"""

rgb = np.empty((0, 4), dtype=np.int64)
label_names = {}

# replace the path to the FreeSurferColorLUT.txt with your own
# in linux you can do: echo $FREESURFER_HOME/FreeSurferColorLUT.txt

with open('/usr/local/freesurfer/FreeSurferColorLUT.txt', 'r') as f:
  raw_lut = f.readlines()

# read and process line by line

pattern = re.compile(r'\d{1,5}[ ]+[a-zA-Z-_0-9*.]+[ ]+\d{1,3}[ ]+\d{1,3}[ ]+\d{1,3}[ ]+\d{1,3}')
for line in raw_lut:
  if pattern.match(line):
    s = line.rstrip().split(' ')
    s = list(filter(None, s))
    rgb = np.append(rgb, np.array([[int(s[0]), int(s[2]), int(s[3]), int(s[4])]]), axis=0)
    label_names[int(s[0])] = s[1]