Tutorial 04: Plot of statistical maps with two thresholds

Example script to plot statistical maps with two different statistical thresholds. The first threshold is plottet as normal, the second threshold is outlined by a white line.

The second_level data is defined by a mask containing e.g. surviving clusters (1’s)

Note: the cortical surface template is needed to segment the clusters.

from surface_plot import plot_stats
import numpy as np

outdir = 'data/second_level/test_figures'
clobber = True
mask = {'left': [], 'right': []}

# Load data
tval_left = np.loadtxt('https://www.dropbox.com/s/5ek63zf5l2iwd8f/tval_left.csv?dl=1')
tval_right = np.loadtxt('https://www.dropbox.com/s/def320uevw5ivsb/tval_right.csv?dl=1')
second_level_left = np.loadtxt('https://www.dropbox.com/s/y93z65g2jx0zs2x/second_level_left.csv?dl=1')
second_level_right = np.loadtxt('https://www.dropbox.com/s/wgp0j0gp35oe41g/second_level_right.csv?dl=1')

tval = {'left': tval_left,
        'right': tval_right}

second_level = {'left': second_level_left.astype(bool),
                'right': second_level_right.astype(bool)}

t_lim = [-5, 5]

mask['left'] = ~np.isnan(tval['left'])
mask['right'] = ~np.isnan(tval['right'])

output = f'{outdir}/second_level.pdf'
plot_stats.plot_tval(tval, output, mask=mask, t_lim=t_lim, second_threshold_mask=second_level, expand_edge=True, clobber=clobber)

output = f'{outdir}/second_level_descrete.pdf'
plot_stats.plot_tval(tval, output, mask=mask, t_lim=t_lim, second_threshold_mask=second_level, plot_discrete=True, clobber=clobber)