Visualizing a single network¶

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Goal¶

Here we are going to take a atlas from templateflow and only visualize the default mode network

In [1]:

# Import packages
import templateflow.api as tf
import netplotbrain
import pandas as pd

# Import packages import templateflow.api as tf import netplotbrain import pandas as pd

In [2]:

# Get template information
template = 'MNI152NLin2009cAsym'
atlas = 'Schaefer2018'
atlas_desc = '400Parcels7Networks'

# Get template information template = 'MNI152NLin2009cAsym' atlas = 'Schaefer2018' atlas_desc = '400Parcels7Networks'

In [3]:

# Get and load the tsv file
atlas_path = tf.get(atlas=atlas,
                    template=template, 
                    desc=atlas_desc, 
                    extension='.tsv')
atlas_df = pd.read_csv(atlas_path, sep='\t')
atlas_df.head()

# Get and load the tsv file atlas_path = tf.get(atlas=atlas, template=template, desc=atlas_desc, extension='.tsv') atlas_df = pd.read_csv(atlas_path, sep='\t') atlas_df.head()

Out[3]:

	index	name	color
0	1	7Networks_LH_Vis_1	#781180
1	2	7Networks_LH_Vis_2	#781181
2	3	7Networks_LH_Vis_3	#781182
3	4	7Networks_LH_Vis_4	#781183
4	5	7Networks_LH_Vis_5	#781184

In [4]:

# Now we need to make a colour argument for the DMN nodes only
# Get which rows are in the default mode network
atlas_df['defaultmode'] = atlas_df['name'].str.contains('Default')
# Set the color column of non DMN nodes to same colour
# Not really necessary cause we make these nods transparant below
atlas_df.loc[~atlas_df['defaultmode'], 'color'] = 'white'

# Now we need to make a colour argument for the DMN nodes only # Get which rows are in the default mode network atlas_df['defaultmode'] = atlas_df['name'].str.contains('Default') # Set the color column of non DMN nodes to same colour # Not really necessary cause we make these nods transparant below atlas_df.loc[~atlas_df['defaultmode'], 'color'] = 'white'

In [5]:

# now plot
netplotbrain.plot(template=template,
                  nodes={
                      'atlas': atlas,
                      'desc': atlas_desc,
                      'resolution': 1},
                  view='preset-3',
                  nodes_df = atlas_df,
                  node_color='color',
                  node_type='parcels',
                  highlight_nodes='defaultmode',
                  highlight_level=1)

# now plot netplotbrain.plot(template=template, nodes={ 'atlas': atlas, 'desc': atlas_desc, 'resolution': 1}, view='preset-3', nodes_df = atlas_df, node_color='color', node_type='parcels', highlight_nodes='defaultmode', highlight_level=1)

Out[5]:

(<Figure size 648x252 with 4 Axes>,
 [<Axes3D: title={'center': 'Left'}>,
  <Axes3D: title={'center': 'Right'}>,
  <Axes3D: title={'center': 'Superior'}>,
  <Axes: >])