usage: __main__.py [-h] [--filtering_mask FILTERING_MASK] [--avg_node_wise]
[--append_json] [--small_world] [--indent INDENT]
[--sort_keys] [-v [{DEBUG,INFO,WARNING}]] [-f]
in_conn_matrix in_length_matrix out_json
Evaluate graph theory measures from connectivity matrices.
A length weighted and a streamline count weighted matrix are required since
some measures require one or the other.
This script evaluates the measures one subject at the time. To generate a
population dictionary (similarly to other scil_connectivity_*.py scripts), use
the --append_json option as well as using the same output filename.
>>> for i in hcp/*/; do scil_connectivity_graph_measures.py ${i}/sc_prob.npy
${i}/len_prob.npy hcp_prob.json --append_json --avg_node_wise; done
Some measures output one value per node, the default behavior is to list
them all into a list. To obtain only the average use the
--avg_node_wise option.
The computed connectivity measures are:
centrality, modularity, assortativity, participation, clustering,
nodal_strength, local_efficiency, global_efficiency, density, rich_club,
path_length, edge_count, omega, sigma
For more details about the measures, please refer to
- https://sites.google.com/site/bctnet/measures
- https://github.com/aestrivex/bctpy/wiki
This script is under the GNU GPLv3 license, for more detail please refer to
https://www.gnu.org/licenses/gpl-3.0.en.html
Formerly: scil_evaluate_connectivity_graph_measures.py
positional arguments:
in_conn_matrix Input connectivity matrix (.npy).
Typically a streamline count weighted matrix.
in_length_matrix Input length weighted matrix (.npy).
out_json Path of the output json.
options:
-h, --help show this help message and exit
--filtering_mask FILTERING_MASK
Binary filtering mask to apply before computing the measures.
--avg_node_wise Return a single value for node-wise measures.
--append_json If the file already exists, will append to the dictionary.
--small_world Compute measure related to small worldness (omega and sigma).
This option is much slower.
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
-f Force overwriting of the output files.
Json options:
--indent INDENT Indent for json pretty print.
--sort_keys Sort keys in output json.
[1] Rubinov, Mikail, and Olaf Sporns. "Complex network measures of brain
connectivity: uses and interpretations." Neuroimage 52.3 (2010):
1059-1069.