comet-toolbox 0.4.8

Dynamic functional connectivity toolbox for multiverse analysis

Comet - A dynamic functional connectivity toolbox for multiverse analysis

Important notes

• This package is at an early stage of development, with frequent changes being made. If you intend to use this package at this stage, I kindly ask that you contact me via the email address in the pyproject.toml file.
• Many features are not yet tested, so there will be bugs (the question is just how many). A comprehensive testing suite and documentation will be added in the near future.

Installation and Usage

It is recommended to use a dedicated Python environment to mitigate the risk of potential version conflicts.

Please refer to the documentation for comprehensive installation and usage instructions. Briefly, installation is possible through the Python Package Index (PyPI) or from the source code in this repository:

pip install comet-toolbox

Usage of the toolbox is then possible through either the GUI:

comet-gui

or (for more versatile usage) through the scripting API. For this, demo scripts are provided as starting points:

• Demo script for calculating dFC
• Demo script for performing multiverse analysis
• Demo script for multiverse analysis example from the preprint (+ additional visualizations)
• Demo script for graph analysis

Current Features

Functional Connectivity	Graph Analysis	Multiverse Analysis
Continuous Sliding Window Correlation Jackknife Correlation Flexible Least Squares Spatial Distance Temporal Derivatives Phase Synchronization Leading Eigenvector Dynamics Wavelet Coherence Edge-centric connectivity State-Based SW Clustering Co-activation Patterns Discrete HMM Continuous HMM Windowless Static Pearson Correlation Partial Correlation Mutual Information	Optimized implementation Average Path Length Global Efficiency Nodal Efficiency Small-World Sigma Small-World Propensity Matching Index Standard Graph Functions Threshold Binarise Symmetrise Negative weights ... BCT Integration All BCT functions can be used seamlessly fory multiverse analysis Many BCT functions are available in the GUI	Simple Definition Forking paths as python dictionary Analysis pipeline template with decision points Generation Universes are created as individual scripts Modular approach Analysis Individual universes Entire multiverse (parallel) Visualization Multiverse summary Multiverse as a network Specification Curve analysis