Netneurotools Guide

NetNeuroTools Guide

Purpose

This skill encodes the complete API and recommended workflows for netneurotools, a Python toolbox for network neuroscience developed by the Network Neuroscience Lab (netneurolab). It covers dataset fetching, brain connectivity metrics, network randomization and null models, community detection, spatial autocorrelation statistics, parcellation interface utilities, and cortical/subcortical surface visualization.

When to Use This Skill

Activate when the user:

• Works with brain connectivity matrices (structural or functional)
• Needs network communication metrics (shortest path, navigation, communicability, search information, diffusion efficiency)
• Wants to generate null/surrogate networks preserving degree, strength, or distance distributions
• Performs community detection or consensus clustering on brain networks
• Computes spatial autocorrelation (Moran's I, Geary's C, Lee's L) on parcellated brain data
• Fetches standard neuroimaging templates (fsaverage, fsLR, CIVET, Conte69) or atlases (Schaefer, Cammoun, Pauli)
• Needs to convert between vertex-level and parcel-level brain data
• Visualizes data on cortical surfaces using PyVista or PySurfer
• Mentions netneurotools, netneurolab, or any function from this toolbox
• Performs structure-function coupling, assortativity analysis, or dominance analysis
• Simulates atrophy spreading on brain networks (SIR model)

Reference Files (Progressive Disclosure)

Installation

bashCopy code
pip install netneurotools

# For PyVista surface plotting (recommended)
pip install netneurotools[pyvista]

# For PySurfer surface plotting (legacy)
pip install netneurotools[pysurfer]

# For numba acceleration
pip install netneurotools[numba]

Core dependencies: numpy>=1.16, scipy>=1.4.0, scikit-learn, matplotlib, nibabel>=3.0.0, nilearn, bctpy, tqdm, neuromaps

Overview Pipeline

Copy code
1. Fetch data       --> netneurotools.datasets (templates, atlases, connectomes)
2. Build networks   --> netneurotools.networks (consensus, thresholding)
3. Analyze metrics  --> netneurotools.metrics (communication, assortativity)
4. Null models      --> netneurotools.networks (randomization, surrogates)
5. Statistics       --> netneurotools.stats (permutation tests, dominance)
6. Spatial stats    --> netneurotools.spatial (Moran's I, Geary's C, Lee's L)
7. Modularity       --> netneurotools.modularity (consensus clustering)
8. Visualize        --> netneurotools.plotting (cortical surfaces, heatmaps)

Quick Start

Fetch Atlas and Template

pythonCopy code
from netneurotools.datasets import fetch_schaefer2018, fetch_fsaverage_curated

# Fetch Schaefer 400-parcel atlas in fsaverage space
parc = fetch_schaefer2018('fsaverage')['400Parcels7Networks']
# parc is a SURFACE namedtuple with fields .L and .R

# Fetch curated fsaverage surfaces
surfaces = fetch_fsaverage_curated('fsaverage5')
# surfaces has keys: 'white', 'pial', 'inflated', 'sphere', 'medial', 'sulc', 'vaavg'
# Each value is a SURFACE namedtuple with fields .L and .R

Consensus Functional Connectivity

pythonCopy code
from netneurotools.networks import func_consensus
import numpy as np

# data: (N_nodes, T_timepoints, S_subjects) array
consensus = func_consensus(data, n_boot=1000, ci=95, seed=42)

Community Detection

pythonCopy code
from netneurotools.modularity import consensus_modularity
import numpy as np

# adjacency: (N, N) non-negative connectivity matrix
consensus, Q_all, zrand_all = consensus_modularity(
    adjacency, gamma=1.5, repeats=100, seed=1234
)

Generate Distance-Preserving Surrogates

pythonCopy code
from netneurotools.networks import match_length_degree_distribution

newB, newW, nr = match_length_degree_distribution(
    W, D, nbins=10, nswap=1000, seed=42
)

Permutation Test for Correlation

pythonCopy code
from netneurotools.stats import permtest_pearsonr, make_correlated_xy

x, y = make_correlated_xy(corr=0.3, size=100, seed=42)
r, p = permtest_pearsonr(x, y, n_perm=5000, seed=42)

Spatial Autocorrelation

pythonCopy code
from netneurotools.spatial import morans_i

I = morans_i(annotation_vector, spatial_weight_matrix)

Plot on Cortical Surface (PyVista)

pythonCopy code
from netneurotools.plotting import pv_plot_surface
import numpy as np

data_L = np.random.random((10242,))
data_R = np.random.random((10242,))
pl = pv_plot_surface(
    (data_L, data_R),
    template="fsaverage5",
    surf="inflated",
    cmap="viridis",
    lighting_style="plastic",
    jupyter_backend="static",
)

Plot Parcellated Data (Shortcut)

pythonCopy code
from netneurotools.plotting import pv_plot_parcellated_data
import numpy as np

data = np.random.rand(400)
pl = pv_plot_parcellated_data(data, 'schaefer400x7', template='fsaverage')

Key Data Structures

Core Modules Quick Reference

Common Pitfalls

1. SURFACE fields are .L and .R, not .lh and .rh. Use surface.L and surface.R to access hemisphere paths.

2. Weight-to-distance conversion must be done before calling distance_wei_floyd or search_information. Common transform: D = -np.log(W / (np.max(W) + 1)).

3. Minimum permutation p-value is 1 / (n_perm + 1). With n_perm=1000, the smallest p-value is ~0.001.

4. consensus_modularity requires non-negative input. Louvain cannot handle negative weights. Set negatives to zero: A[A < 0] = 0.

5. struct_consensus hemiid encoding: 0 = right hemisphere, 1 = left hemisphere.

6. pv_plot_surface data format: When hemi='both', vertex_data can be a tuple (left, right) or a single concatenated array. Data length must match template vertex count.

7. Data directory: All fetch functions default to ~/nnt-data. Override with data_dir= parameter or set NNT_DATA environment variable.

8. match_length_degree_distribution recommended nswap: Use nswap = nnodes * 20 for adequate randomization.

9. strength_preserving_rand_sa frac parameter must be between 0 and 1. It controls temperature decrease per annealing stage.

10. parcels_to_vertices and vertices_to_parcels support .annot, .gii, and .dlabel.nii parcellation files. For .dlabel.nii, pass a single file path; for .annot or .gii, pass a tuple of (left, right) paths.

11. Numba acceleration is available for spatial stats, weighted correlation, and some metrics. Install numba for significant speedups on large datasets.

12. Headless rendering with PyVista: set os.environ["VTK_DEFAULT_OPENGL_WINDOW"] = "vtkOSOpenGLRenderWindow" before importing pyvista.