<commit_before>#!/usr/bin/env python

#=============================================================================
# Created by <NAME>
# September 2014
# Contact: <EMAIL>
#=============================================================================

#=============================================================================
# IMPORTS
#=============================================================================
from __future__ import print_function

import os
import sys
import argparse
import numpy as np

import pandas as pd
import nibabel as nib
from surfer import Brain
import seaborn as sns

import itertools as it

import matplotlib.pylab as plt
import matplotlib.image as mpimg
import matplotlib.gridspec as gridspec

import matplotlib.colors as mcolors
import matplotlib.cm as cm

#=============================================================================
# FUNCTIONS
#=============================================================================
def setup_argparser():
    '''
    Code to read in arguments from the command line
    Aso allows you to change some settings
    '''
    # Build a basic parser.
    help_text = ('Plot a single value for each region in the NSPN 500 parcellation of the fsaverage surface')

    sign_off = 'Author: <NAME> <<EMAIL>>'

    parser = argparse.ArgumentParser(description=help_text, epilog=sign_off)

    # Now add the arguments
    parser.add_argument(dest='roi_file',
                            type=str,
                            metavar='roi_file',
                            help='roi file containing list of measure values - one for each region - csv format')

    parser.add_argument('--annot_name',
                            type=str,
                            metavar='annot_name',
                            help='name of annot file that contains the parcellation',
                            default='500.aparc')

    parser.add_argument('--fsaverageid',
                            type=str,
                            metavar='fsaverage_id',
                            help='FSaverage subject id',
                            default='fsaverageSubP')

    parser.add_argument('-sd', '--subjects_dir',
                            type=str,
                            metavar='subjects_dir',
                            help='freesurfer subjects dir',
                            default=os.path.join(os.path.dirname(sys.argv[0]),
                                                 '..', 'required_data'))

    parser.add_argument('-c', '--cmap',
                            type=str,
                            metavar='cmap',
                            help='colormap',
                            default='RdBu_r')

    parser.add_argument('-c2', '--cmap2',
                            type=str,
                            metavar='cmap2',
                            help='colormap for the second overlay',<commit_msg>Add a little extra to the help text<commit_after>#!/usr/bin/env python

#=============================================================================
# Created by <NAME>
# September 2014
# Contact: <EMAIL>
#=============================================================================

#=============================================================================
# IMPORTS
#=============================================================================
from __future__ import print_function

import os
import sys
import argparse
import numpy as np

import pandas as pd
import nibabel as nib
from surfer import Brain
import seaborn as sns

import itertools as it

import matplotlib.pylab as plt
import matplotlib.image as mpimg
import matplotlib.gridspec as gridspec

import matplotlib.colors as mcolors
import matplotlib.cm as cm

#=============================================================================
# FUNCTIONS
#=============================================================================
def setup_argparser():
    '''
    Code to read in arguments from the command line
    Aso allows you to change some settings
    '''
    # Build a basic parser.
    help_text = ('Plot a single value for each region in the NSPN 500 parcellation of the fsaverage surface')

    sign_off = 'Author: <NAME> <<EMAIL>>'

    parser = argparse.ArgumentParser(description=help_text, epilog=sign_off)

    # Now add the arguments
    parser.add_argument(dest='roi_file',
                            type=str,
                            metavar='roi_file',
                            help='roi file containing list of measure values - one for each region - csv format')

    parser.add_argument('--annot_name',
                            type=str,
                            metavar='annot_name',
                            help=('name of annot file that contains the parcellation\n' +
                                  'the code has been tested with aparc, 500.aparc,\n' +
                                  'economo and HCP annot files that are shipped within\n' +
                                  'the required_data/fsaverageSubP directory'),
                            default='500.aparc')

    parser.add_argument('--fsaverageid',
                            type=str,
                            metavar='fsaverage_id',
                            help='FSaverage subject id',
                            default='fsaverageSubP')

    parser.add_argument('-sd', '--subjects_dir',
                            type=str,
                            metavar='subjects_dir',
                            help='freesurfer subjects dir',
                            default=os.path.join(os.path.dirname(sys.argv[0]),
                                                 '..', 'required_data'))

    parser.add_argument('-c', '--cmap',
                            type=str,
                            metavar='cmap',
                            help='colormap',
                            default='RdBu_r')

    parser.add_argument('-c2', '--cmap2',
                            type=str,
                            metavar='cmap2',
                            help='colormap for the second overlay',
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