# Here we define the parcellation scheme and the number of tracks to produce
parcellation_scheme = 'NativeFreesurfer'
cmp_config = cmp.configuration.PipelineConfiguration()
cmp_config.parcellation_scheme = parcellation_scheme
l1pipeline.inputs.connectivity.inputnode.resolution_network_file = cmp_config._get_lausanne_parcellation(parcellation_scheme)['freesurferaparc']['node_information_graphml']
l1pipeline.run()
l1pipeline.write_graph(format='eps', graph2use='flat')
# The second-level pipeline is created here
l2pipeline = create_merge_networks_by_group_workflow(group_list, group_id, data_dir, subjects_dir, output_dir)
l2pipeline.run()
l2pipeline.write_graph(format='eps', graph2use='flat')
"""
Now that the for loop is complete there are two grouped CFF files each containing the appropriate subjects.
It is also convenient to have every subject in a single CFF file, so that is what the third-level pipeline does.
"""
l3pipeline = create_merge_group_networks_workflow(group_list, data_dir, subjects_dir, output_dir, title)
l3pipeline.run()
l3pipeline.write_graph(format='eps', graph2use='flat')
"""
The fourth and final workflow averages the networks and saves them in another CFF file
"""
l4pipeline = create_average_networks_by_group_workflow(group_list, data_dir, subjects_dir, output_dir, title)
l4pipeline.run()
l4pipeline.write_graph(format='eps', graph2use='flat')
l1pipeline.inputs.connectivity.inputnode.resolution_network_file = cmp_config._get_lausanne_parcellation(
parcellation_scheme)['freesurferaparc']['node_information_graphml']
l1pipeline.run()
l1pipeline.write_graph(format='eps', graph2use='flat')
# The second-level pipeline is created here
l2pipeline = create_merge_networks_by_group_workflow(
group_list, group_id, data_dir, subjects_dir, output_dir)
l2pipeline.run()
l2pipeline.write_graph(format='eps', graph2use='flat')
"""
Now that the for loop is complete there are two grouped CFF files each containing the appropriate subjects.
It is also convenient to have every subject in a single CFF file, so that is what the third-level pipeline does.
"""
l3pipeline = create_merge_group_networks_workflow(group_list, data_dir,
subjects_dir, output_dir,
title)
l3pipeline.run()
l3pipeline.write_graph(format='eps', graph2use='flat')
"""
The fourth and final workflow averages the networks and saves them in another CFF file
"""
l4pipeline = create_average_networks_by_group_workflow(group_list, data_dir,
subjects_dir,
output_dir, title)
l4pipeline.run()
l4pipeline.write_graph(format='eps', graph2use='flat')